I attach a log with the output of 
/opt/scripts/tools/eMMC/beaglebone-black-make-microSD-flasher-from-eMMC.sh 
and a fragment of output of e2fsck -f /dev/mmcblk0p1.

BBB can boot from it, then it gets slowly worse until halt. Still, BBB 
works normally with its eMMC. One of the reasons might be, that 
/dev/mmcblk0p1 is reported as having 4GB or 16GB, depending on the software.



Unattached inode 793363
Connect to /lost+found? yes

Inode 793363 ref count is 2, should be 1.  Fix? yes

Unattached inode 793364
Connect to /lost+found? yes

Inode 793364 ref count is 2, should be 1.  Fix? yes

Unattached inode 793365
Connect to /lost+found? yes

Inode 793365 ref count is 2, should be 1.  Fix? yes

Unattached inode 793366
Connect to /lost+found? yes

Inode 793366 ref count is 2, should be 1.  Fix? yes

Unattached inode 793367
Connect to /lost+found? yes

Inode 793367 ref count is 2, should be 1.  Fix? yes

Unattached inode 793368
Connect to /lost+found? yes

Inode 793368 ref count is 2, should be 1.  Fix? yes

Unattached inode 793369
Connect to /lost+found? yes

Inode 793369 ref count is 2, should be 1.  Fix? yes

Unattached inode 793370
Connect to /lost+found? yes

Inode 793370 ref count is 2, should be 1.  Fix? yes

Inode 793421 ref count is 1, should be 2.  Fix? yes

Inode 794552 ref count is 6, should be 4.  Fix? yes

Inode 794553 ref count is 6, should be 4.  Fix? yes

Inode 794554 ref count is 6, should be 4.  Fix? yes

Inode 794555 ref count is 6, should be 4.  Fix? yes

Unattached inode 794592
Connect to /lost+found? yes

Inode 794592 ref count is 2, should be 1.  Fix? yes

Unattached inode 794600
Connect to /lost+found? yes

Inode 794600 ref count is 2, should be 1.  Fix? yes

Unattached inode 794601
Connect to /lost+found? yes

Inode 794601 ref count is 2, should be 1.  Fix? yes

Unattached inode 794605
Connect to /lost+found? yes

Inode 794605 ref count is 2, should be 1.  Fix? yes


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/opt/scripts/tools/eMMC/beaglebone-black-make-microSD-flasher-from-eMMC.sh 

================================================================================
Starting eMMC Flasher from microSD media
Version: [1.20180412: all ssh regneration override...]
================================================================================

================================================================================
Prepare environment for flashing
Starting at Fri Nov  4 11:31:15 UTC 2016
----------------------------------------
==> sysctl: vm.min_free_kbytes=[2653]
==> sysctl: setting: [sysctl -w vm.min_free_kbytes=16384]
vm.min_free_kbytes = 16384
----------------------------------------
==> Determining root drive
==> console=ttyO0,115200n8 bone_capemgr.uboot_capemgr_enabled=1 
root=/dev/mmcblk1p1 ro rootfstype=ext4 rootwait coherent_pool=1M net.ifnames=0 
quiet
----------------------------------------
==> root_drive=[/dev/mmcblk1p1]
====> Root drive identified at /dev/mmcblk1p1
==> Determining boot drive
==> Figuring out Source and Destination devices
====> Source identified: [/dev/mmcblk1]
====> Destination identified: [/dev/mmcblk0]
====> Unmounting auto-mounted partitions
==> Figuring out machine
====> Machine is TI_AM335x_BeagleBone_Blue
====> Machine is compatible with BeagleBone Black
================================================================================
5 4 3 2 1 

================================================================================
Checking running system
==> Copying: [/dev/mmcblk1] -> [/dev/mmcblk0]
==> lsblk:
----------------------------------------
NAME         MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
mmcblk0      179:0    0 14.9G  0 disk 
└─mmcblk0p1  179:1    0 14.9G  0 part 
mmcblk1      179:8    0  3.6G  0 disk 
└─mmcblk1p1  179:9    0  3.6G  0 part /
mmcblk1boot0 179:16   0    4M  1 disk 
mmcblk1boot1 179:24   0    4M  1 disk 
mmcblk1rpmb  179:32   0    4M  0 disk 
----------------------------------------
==> df -h | grep rootfs:
----------------------------------------
==> updating: /boot/initrd.img-4.14.71-ti-r80
update-initramfs: Generating /boot/initrd.img-4.14.71-ti-r80
WARNING: Setting CRYPTSETUP in /etc/initramfs-tools/initramfs.conf is 
deprecated and will stop working in the future. Use 
/etc/cryptsetup-initramfs/conf-hook instead.
cryptsetup: WARNING: failed to detect canonical device of /dev/mmcblk1p1
cryptsetup: WARNING: could not determine root device from /etc/fstab
==> Giving you time to check...
10 9 8 7 6 5 4 3 2 1 
================================================================================

================================================================================
Preparing drives

----------------------------------------
==> Erasing: /dev/mmcblk0
----------------------------------------
108+0 records in
108+0 records out
113246208 bytes (113 MB, 108 MiB) copied, 14.4979 s, 7.8 MB/s
----------------------------------------
108+0 records in
108+0 records out
113246208 bytes (113 MB, 108 MiB) copied, 5.1432 s, 22.0 MB/s
----------------------------------------
==> Erasing: /dev/mmcblk0 complete
----------------------------------------

----------------------------------------
==> Loading /boot/SOC.sh
************************************************************
#!/bin/sh
format=1.0

board=am335x_evm

bootloader_location=dd_spl_uboot_boot
bootrom_gpt=

dd_spl_uboot_count=1
dd_spl_uboot_seek=1
dd_spl_uboot_conf=notrunc
dd_spl_uboot_bs=128k
dd_spl_uboot_backup=/opt/backup/uboot/MLO

dd_uboot_count=2
dd_uboot_seek=1
dd_uboot_conf=notrunc
dd_uboot_bs=384k
dd_uboot_backup=/opt/backup/uboot/u-boot.img

boot_fstype=ext4
conf_boot_startmb=4
conf_boot_endmb=
sfdisk_fstype=L

boot_label=BOOT
rootfs_label=rootfs

#Kernel
dtb=
serial_tty=ttyO0
usbnet_mem=

#Advanced options
#disable_ssh_regeneration=true

************************************************************
==> Loaded

----------------------------------------

================================================================================
Writing bootloader to [/dev/mmcblk0]
----------------------------------------
==> Figuring out options for SPL U-Boot copy ...
===> Will use : count=1 seek=1 conv=notrunc bs=128k
==> Figuring out options for U-Boot copy ...
===> Will use : count=2 seek=1 conv=notrunc bs=384k
==> Copying SPL U-Boot with dd if=/opt/backup/uboot/MLO of=/dev/mmcblk0 count=1 
seek=1 conv=notrunc bs=128k
------------------------------------------------------------
0+1 records in
0+1 records out
90932 bytes (91 kB, 89 KiB) copied, 0.0179716 s, 5.1 MB/s
------------------------------------------------------------
==> Copying U-Boot with dd if=/opt/backup/uboot/u-boot.img of=/dev/mmcblk0 
count=2 seek=1 conv=notrunc bs=384k
------------------------------------------------------------
1+1 records in
1+1 records out
447372 bytes (447 kB, 437 KiB) copied, 0.0897527 s, 5.0 MB/s
------------------------------------------------------------
Writing bootloader completed
================================================================================

================================================================================
Partitionning /dev/mmcblk0
----------------------------------------
sfdisk: [2.26.x or greater]
==> sfdisk parameters:
sfdisk: [sfdisk from util-linux 2.29.2]
sfdisk: [sfdisk --force /dev/mmcblk0]
sfdisk: [4M,,L,*]
==> Partitionning
------------------------------------------------------------
Checking that no-one is using this disk right now ... OK

Disk /dev/mmcblk0: 14.9 GiB, 15980298240 bytes, 31211520 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

>>> Created a new DOS disklabel with disk identifier 0xc2b76c31.
/dev/mmcblk0p1: Created a new partition 1 of type 'Linux' and of size 14.9 GiB.
/dev/mmcblk0p2: Done.

New situation:

Device         Boot Start      End  Sectors  Size Id Type
/dev/mmcblk0p1 *     8192 31211519 31203328 14.9G 83 Linux

The partition table has been altered.
Calling ioctl() to re-read partition table.
Syncing disks.
------------------------------------------------------------

==> Partitionning Completed
==> Generated Partitions:
------------------------------------------------------------
Disk /dev/mmcblk0: 14.9 GiB, 15980298240 bytes, 31211520 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0xc2b76c31

Device         Boot Start      End  Sectors  Size Id Type
/dev/mmcblk0p1 *     8192 31211519 31203328 14.9G 83 Linux
------------------------------------------------------------
================================================================================

================================================================================
Preparing future rootfs to receive files
----------------------------------------

==> Formatting rootfs with mkfs.ext4  -O ^metadata_csum,^64bit /dev/mmcblk0p1 
-L rootfs
--------------------------------------------------------------------------------

mke2fs 1.43.4 (31-Jan-2017)
Discarding device blocks: done                            
Creating filesystem with 3900416 4k blocks and 975360 inodes
Filesystem UUID: b0841258-7b45-487b-82cc-ae1dd2d71bfe
Superblock backups stored on blocks: 
        32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (16384 blocks): done
Writing superblocks and filesystem accounting information: done   

--------------------------------------------------------------------------------
==> Formatting rootfs: /dev/mmcblk0p1 complete
==> Creating temporary rootfs directory (/tmp/rootfs)
==> Mounting /dev/mmcblk0p1 to /tmp/rootfs

================================================================================

================================================================================
Copying: Current rootfs to /dev/mmcblk0p1
----------------------------------------
==> rsync: / -> /tmp/rootfs
----------------------------------------
          2.73G  99%    3.71MB/s    0:11:42 (xfr#95114, to-chk=0/112490)   ^[[B
----------------------------------------
==> Copying: Kernel modules
===> Creating directory for modules
===> rsync: /lib/modules/4.14.71-ti-r80/ -> 
/tmp/rootfs/lib/modules/4.14.71-ti-r80/
----------------------------------------
         46.29M 100%    3.31MB/s    0:00:13 (xfr#2310, to-chk=0/2685)   
----------------------------------------
Copying: Current rootfs to /dev/mmcblk0p1 complete
================================================================================

================================================================================
Final System Tweaks:
----------------------------------------

==> Generating: /etc/fstab
===> /etc/fstab generated
****************************************
# /etc/fstab: static file system information.
#
/dev/mmcblk0p1  /  ext4  noatime,errors=remount-ro  0  1
debugfs  /sys/kernel/debug  debugfs  defaults  0  0
****************************************

==> /boot/uEnv.txt: enabling eMMC flasher script
****************************************
#Docs: http://elinux.org/Beagleboard:U-boot_partitioning_layout_2.0

uname_r=4.14.71-ti-r80
#uuid=
#dtb=

###U-Boot Overlays###
###Documentation: 
http://elinux.org/Beagleboard:BeagleBoneBlack_Debian#U-Boot_Overlays
###Master Enable
enable_uboot_overlays=1
###
###Overide capes with eeprom
#uboot_overlay_addr0=/lib/firmware/<file0>.dtbo
#uboot_overlay_addr1=/lib/firmware/<file1>.dtbo
#uboot_overlay_addr2=/lib/firmware/<file2>.dtbo
#uboot_overlay_addr3=/lib/firmware/<file3>.dtbo
###
###Additional custom capes
#uboot_overlay_addr4=/lib/firmware/<file4>.dtbo
#uboot_overlay_addr5=/lib/firmware/<file5>.dtbo
#uboot_overlay_addr6=/lib/firmware/<file6>.dtbo
#uboot_overlay_addr7=/lib/firmware/<file7>.dtbo
###
###Custom Cape
#dtb_overlay=/lib/firmware/<file8>.dtbo
###
###Disable auto loading of virtual capes (emmc/video/wireless/adc)
#disable_uboot_overlay_emmc=1
#disable_uboot_overlay_video=1
#disable_uboot_overlay_audio=1
#disable_uboot_overlay_wireless=1
#disable_uboot_overlay_adc=1
###
###PRUSS OPTIONS
###pru_rproc (4.4.x-ti kernel)
#uboot_overlay_pru=/lib/firmware/AM335X-PRU-RPROC-4-4-TI-00A0.dtbo
###pru_rproc (4.14.x-ti kernel)
uboot_overlay_pru=/lib/firmware/AM335X-PRU-RPROC-4-14-TI-00A0.dtbo
###pru_uio (4.4.x-ti, 4.14.x-ti & mainline/bone kernel)
#uboot_overlay_pru=/lib/firmware/AM335X-PRU-UIO-00A0.dtbo
###
###Cape Universal Enable
enable_uboot_cape_universal=1
###
###Debug: disable uboot autoload of Cape
#disable_uboot_overlay_addr0=1
#disable_uboot_overlay_addr1=1
#disable_uboot_overlay_addr2=1
#disable_uboot_overlay_addr3=1
###
###U-Boot fdt tweaks... (60000 = 384KB)
#uboot_fdt_buffer=0x60000
###U-Boot Overlays###

cmdline=coherent_pool=1M net.ifnames=0 quiet

#In the event of edid real failures, uncomment this next line:
#cmdline=coherent_pool=1M net.ifnames=0 quiet video=HDMI-A-1:1024x768@60e

#Use an overlayfs on top of a read-only root filesystem:
#cmdline=coherent_pool=1M net.ifnames=0 quiet overlayroot=tmpfs

##enable bbbl: eMMC Flasher:
#cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3-bbbl.sh

#cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh
cmdline=init=/opt/scripts/tools/eMMC/init-eMMC-flasher-v3.sh
****************************************

================================================================================
Tearing down future rootfs
----------------------------------------

==> Unmounting /tmp/rootfs
================================================================================
================================================================================
Tearing Down script environment
==> Stopping Cylon LEDs ...
==> Setting LEDs to 
==> Force writeback of eMMC buffers by Syncing: /dev/mmcblk0
/opt/scripts/tools/eMMC/functions.sh: line 280:  4276 Terminated              
cylon_leds
----------------------------------------
100000+0 records in
100000+0 records out
51200000 bytes (51 MB, 49 MiB) copied, 2.66634 s, 19.2 MB/s
----------------------------------------
===> Syncing: /dev/mmcblk0 complete
==> This script took 833 seconds to run
================================================================================

==> Setting LEDs to 
==> Displaying mount points
--------------------------------------------------------------------------------
sysfs on /sys type sysfs (rw,nosuid,nodev,noexec,relatime)
proc on /proc type proc (rw,nosuid,nodev,noexec,relatime)
udev on /dev type devtmpfs 
(rw,nosuid,relatime,size=220088k,nr_inodes=55022,mode=755)
devpts on /dev/pts type devpts 
(rw,nosuid,noexec,relatime,gid=5,mode=620,ptmxmode=000)
tmpfs on /run type tmpfs (rw,nosuid,noexec,relatime,size=49508k,mode=755)
/dev/mmcblk1p1 on / type ext4 (rw,noatime,errors=remount-ro,data=ordered)
securityfs on /sys/kernel/security type securityfs 
(rw,nosuid,nodev,noexec,relatime)
tmpfs on /dev/shm type tmpfs (rw,nosuid,nodev)
tmpfs on /run/lock type tmpfs (rw,nosuid,nodev,noexec,relatime,size=5120k)
tmpfs on /sys/fs/cgroup type tmpfs (ro,nosuid,nodev,noexec,mode=755)
cgroup on /sys/fs/cgroup/systemd type cgroup 
(rw,nosuid,nodev,noexec,relatime,xattr,release_agent=/lib/systemd/systemd-cgroups-agent,name=systemd)
cgroup on /sys/fs/cgroup/devices type cgroup 
(rw,nosuid,nodev,noexec,relatime,devices)
cgroup on /sys/fs/cgroup/net_cls,net_prio type cgroup 
(rw,nosuid,nodev,noexec,relatime,net_cls,net_prio)
cgroup on /sys/fs/cgroup/freezer type cgroup 
(rw,nosuid,nodev,noexec,relatime,freezer)
cgroup on /sys/fs/cgroup/cpu,cpuacct type cgroup 
(rw,nosuid,nodev,noexec,relatime,cpu,cpuacct)
cgroup on /sys/fs/cgroup/perf_event type cgroup 
(rw,nosuid,nodev,noexec,relatime,perf_event)
cgroup on /sys/fs/cgroup/memory type cgroup 
(rw,nosuid,nodev,noexec,relatime,memory)
cgroup on /sys/fs/cgroup/pids type cgroup (rw,nosuid,nodev,noexec,relatime,pids)
cgroup on /sys/fs/cgroup/blkio type cgroup 
(rw,nosuid,nodev,noexec,relatime,blkio)
systemd-1 on /proc/sys/fs/binfmt_misc type autofs 
(rw,relatime,fd=34,pgrp=1,timeout=0,minproto=5,maxproto=5,direct,pipe_ino=15346)
mqueue on /dev/mqueue type mqueue (rw,relatime)
debugfs on /sys/kernel/debug type debugfs (rw,relatime)
fusectl on /sys/fs/fuse/connections type fusectl (rw,relatime)
configfs on /sys/kernel/config type configfs (rw,relatime)
tmpfs on /run/user/1000 type tmpfs 
(rw,nosuid,nodev,relatime,size=49504k,mode=700,uid=1000,gid=1000)
--------------------------------------------------------------------------------

================================================================================
eMMC has been flashed: please wait for device to power down.
================================================================================
Calling shutdown
==> Setting LEDs to 

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