I know this is 1.5 years later, but I seem to be running into the same 
issue and am having a hard time finding anything as to how to solve this:
https://groups.google.com/d/msg/beagleboard/IeLSZ19NbMU/xeND-QH0AAAJ

Interestingly, hot plug for the uSD card works for me on a 3.8.13 kernel 
under Debian Wheezy (3.8.13-bone79 to be precise), so this must have been 
fixed in the meantime. However, it fails to work on a 4.1.15 kernel under 
Ubuntu 14.04.3 (4.1.15-ti-r40 to be precise). Would this be because it 
wasn't compiled into the kernel?

On Monday, July 29, 2013 at 2:32:12 AM UTC-4, William Hermans wrote:
>
> By the by Patrick, this happened to me while booted off a USB hard drive. 
> However, the USB boot process in my case does require MLO, u-boot.img, and 
> uEnv.txt to be on the SD card. Of course this also means the SD card is 
> inserted at boot time as well.
>
>
> On Sun, Jul 28, 2013 at 11:30 PM, William Hermans <yyr...@gmail.com 
> <javascript:>> wrote:
>
>> All things being equal, if the hotplug issues were not causing problems. 
>> Removing then re-inserting the drive in of its self should not cause any 
>> problems. 
>>
>> At least I have demonstrated this to myself several times by restarting 
>> an NFS server ( which my beaglebone black has booted from in the past ). 
>> While the Beaglebone black kept running. Of course I did not issue any 
>> commands until the server was back up, and live again.
>>
>> Anyhow, perhaps I will attempt to dig into this deeper myself at some 
>> later point. But I am not sure if I would be able to find the exact problem.
>>
>>
>> On Sun, Jul 28, 2013 at 10:01 PM, evilwulfie <evilw...@gmail.com 
>> <javascript:>> wrote:
>>
>>> no kidding
>>> i use a SD card to boot from
>>>
>>>
>>> On 7/28/2013 9:52 PM, Patrick wrote:
>>>
>>> Wulf Man,
>>>   What is this "boot device" to which you refer?
>>>
>>> If you're talking about the rootfs, then yes it would be bad to remove 
>>> that, but my rootfs is on the eMMC.
>>>
>>> If you think that having an SD card in at boot makes it automatically 
>>> the rootfs, then you're wrong. The default uboot config looks for an SD 
>>> card and if it finds one looks for a uEnv.txt file on it; after that, uboot 
>>> is done with the SD card, unless that uEnv.txt tells it to boot from SD.
>>>
>>> Patrick
>>>
>>> On Sunday, July 28, 2013 2:22:32 PM UTC-4, Wulf Man wrote: 
>>>>
>>>> I cannot see how removing the SD card that is the boot device can be a 
>>>> good thing for a linux kernel
>>>> If it was just SD card storage and you issue the unmount command sure
>>>> or if the kernel has some kind of hot swap mechanism to allow that 
>>>>
>>>>
>>>> am i wrong that removing the boot device is a bad thing ? 
>>>>
>>>>
>>>>
>>>>
>>>> On 7/28/2013 11:03 AM, William Hermans wrote:
>>>>
>>>> Just repeated what I did earlier( twice ), that is removed sd card 
>>>> reinserted issued some disk utility commands, and nothing. BBB is still up 
>>>> and running. However, running blkid, and other disk utilities when the SD 
>>>> card is out did not change the output. Read: it seems the system still 
>>>> thinks it is plugged in, when it is in fact removed.
>>>>
>>>>
>>>> On Sun, Jul 28, 2013 at 10:41 AM, William Hermans <yyr...@gmail.com> 
>>>> wrote:
>>>>
>>>>> I should have said earlier that /var/log/messages does not seem to 
>>>>> have any related messages either. Although I have not grepped yet for 
>>>>> exactness
>>>>>
>>>>>
>>>>> On Sun, Jul 28, 2013 at 10:37 AM, William Hermans <yyr...@gmail.com> 
>>>>> wrote:
>>>>>
>>>>>> I stand corrected. It looks like now, I also have the same issue now. 
>>>>>> I do not exactly get a panic message. In fact I get no message at all. 
>>>>>> However the beaglebone black that has been runing fine for days straight 
>>>>>> suddenly started acting funny after  i removed the SD card, and 
>>>>>> reinserted 
>>>>>> it. 
>>>>>>
>>>>>> df -h would not function at all, but uname -a did. blkid would not 
>>>>>> work either, I guess I'll have to hook up my serial debug device again. 
>>>>>> ALthough I am not sure if that will help. THe problem seems to be silent 
>>>>>> for me. Perhaps using the $optargs debug parameter in uEnv.txt will help 
>>>>>> ?
>>>>>>
>>>>>> This is new however. This has not happened for me in the past, so it 
>>>>>> may be one of the latest kernel version I've built ?
>>>>>>
>>>>>> root@arm:~# uname -a
>>>>>> Linux arm 3.8.13-bone21 #1 SMP Sat Jun 15 19:36:33 MST 2013 armv7l 
>>>>>> GNU/Linux
>>>>>>
>>>>>> This is debian wheezy by the way, and I boot from a USB hard drive. 
>>>>>> Using ethernet for LAN connection, and powered via USB 3.0. The USB hard 
>>>>>> drive is an external case + seagate baracuda ATA that is self powered.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sun, Jul 28, 2013 at 2:49 AM, Patrick <adapt...@gmail.com> wrote:
>>>>>>
>>>>>>> William,
>>>>>>>   The only hotplug problems I've had with USB have been due to it 
>>>>>>> taking too much current, or plugging in a hub that feeds power back to 
>>>>>>> the 
>>>>>>> host. Once I switched to a powered hub that does not feed anything 
>>>>>>> back, 
>>>>>>> everything was fine; the same issue affects the pi, and the same hub 
>>>>>>> solves 
>>>>>>> that problem on the pi. Now I can plug/unplug USB devices, including 
>>>>>>> storage, optical mice etc, without any problem.
>>>>>>>
>>>>>>> This is a completely separate issue.
>>>>>>>
>>>>>>> Are you saying that if you have a microSD card attached at boot, and 
>>>>>>> you remove it post-boot, you don't get a kernel panic 1 minute later? 
>>>>>>> What 
>>>>>>> happens for you when you run a blkid or partprobe? Does it still think 
>>>>>>> the 
>>>>>>> card is in there?
>>>>>>>
>>>>>>> Patrick
>>>>>>>
>>>>>>>
>>>>>>> On Sunday, July 28, 2013 3:11:16 AM UTC-4, William Hermans wrote: 
>>>>>>>>
>>>>>>>> Well hotplug is a known issue, and afaik is a kernel related 
>>>>>>>> problem. This effects the SD slot, and USB. Never heard of or 
>>>>>>>> experienced a 
>>>>>>>> kernel panic though. Not saying I do not believe you, just saying that 
>>>>>>>> I 
>>>>>>>> have hot-plugged both USB and the SD card slot and have not personally 
>>>>>>>> experienced this. What happens for me, the device in question, may 
>>>>>>>> work for 
>>>>>>>> one more hot-plug, but will fail any further attempts.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sat, Jul 27, 2013 at 9:22 PM, Patrick <adapt...@gmail.com> 
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Furthermore, your statement about mmcblk0 is incorrect. If the 
>>>>>>>>> microSD card is present, I don't have to boot from it. I can 
>>>>>>>>> interrupt 
>>>>>>>>> uboot, run a simple sequence of commands, and boot from eMMC without 
>>>>>>>>> ever 
>>>>>>>>> touching the microSD card, and the microSD card still shows up as 
>>>>>>>>> mmcblk0.
>>>>>>>>> And I really don't care whether the microSD displaces eMMC and 
>>>>>>>>> causes device renaming (that is a lame problem, but solvable by UUIDs 
>>>>>>>>> and/or udev rules). But if I can't insert/remove microSD cards after 
>>>>>>>>> boot 
>>>>>>>>> time, I may as well give up on microSD altogether. 
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Patrick
>>>>>>>>>
>>>>>>>>> On Saturday, July 27, 2013 11:13:54 PM UTC-4, William Hermans 
>>>>>>>>> wrote: 
>>>>>>>>>>
>>>>>>>>>> First, the media which is booted from shows up as mmcblk0 always 
>>>>>>>>>>> on the BBB. So it does not matter if it is an SD card or eMMC. Well 
>>>>>>>>>>> this 
>>>>>>>>>>> only applies to SD vs eMMC. If you boot from a network, or USB it 
>>>>>>>>>>> might be 
>>>>>>>>>>> different. 
>>>>>>>>>>>
>>>>>>>>>>> As for the boot order, or what the BBB boots from this can be 
>>>>>>>>>>> and often is determined by uEnv.txt.. Although pressing and holding 
>>>>>>>>>>> the 
>>>>>>>>>>> boot button when booting cant change this. In order to boot from 
>>>>>>>>>>> eMMC while 
>>>>>>>>>>> an SD card is inserted, you need to have a properly configured 
>>>>>>>>>>> uEnv.txt 
>>>>>>>>>>> file variables. something such as this:
>>>>>>>>>>>
>>>>>>>>>>> mmcdev=1
>>>>>>>>>>> bootpart=1:2
>>>>>>>>>>> mmcroot=/dev/mmcblk1p2 ro
>>>>>>>>>>>
>>>>>>>>>>> In your uEnv.txt file should allow you to boot from the eMMC with 
>>>>>>>>>>> an SD card inserted into the SD card slot.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>> -- 
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>>>>>>>  
>>>>>>>
>>>>>>
>>>>>>
>>>>>
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