The good news (?) is that this seems easy to reproduce; editing any file
in emacs seems to do the trick:

  https://pastebin.ubuntu.com/p/XydrSqfkfX/

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https://bugs.launchpad.net/bugs/1879196

Title:
  'shifted' (shiftfs) FS mount became inconsistent with host FS;
  resolved by dropping caches

Status in linux package in Ubuntu:
  Incomplete

Bug description:
  On Ubuntu 20.04 with linux-image-5.4.0-30-generic from the Canonical
  Kernel Team's proposed PPA, I ran into the following problem with
  using a shiftfs 'shifted' ext4 FS mount inside a LXD container.

  On the host, I created a file (in emacs) that was in no way special
  (single line text file):

  🙂 james@malefic:~/projects/ethq/deb$ stat 
ethq-0.6.1~git2020517/debian/ethq.install
    File: ethq-0.6.1~git2020517/debian/ethq.install
    Size: 15              Blocks: 8          IO Block: 4096   regular file
  Device: fd01h/64769d    Inode: 7085913     Links: 1
  Access: (0664/-rw-rw-r--)  Uid: ( 1000/   james)   Gid: ( 1000/   james)
  Access: 2020-05-17 22:48:36.274528130 +0100
  Modify: 2020-05-17 22:37:17.676232019 +0100
  Change: 2020-05-17 22:37:17.676232019 +0100
   Birth: -
  🙂 james@malefic:~/projects/ethq/deb$ stat ethq-0.6.1~git2020517/debian/rules

  But in the container, I saw this:

  ubuntu@ethq-build:~/ethq/deb/ethq-0.6.1~git2020517$ ls -l debian/
  ls: cannot access 'debian/ethq.install': No such file or directory
  total 20
  -rw-rw-r-- 1 ubuntu ubuntu 150 May 17 21:25 changelog
  -rw-r--r-- 1 ubuntu ubuntu   2 May 17 21:36 compat
  -rw-rw-r-- 1 ubuntu ubuntu 514 May 17 21:14 control
  -rw-rw-r-- 1 ubuntu ubuntu 720 May 17 21:20 copyright
  -????????? ? ?      ?        ?            ? ethq.install
  -rwxr-xr-x 1 ubuntu ubuntu  30 May 17 21:35 rules
  ubuntu@ethq-build:~/ethq/deb/ethq-0.6.1~git2020517$ stat debian/ethq.install
  stat: cannot stat 'debian/ethq.install': No such file or directory
  ubuntu@ethq-build:~/ethq/deb/ethq-0.6.1~git2020517$ 

  On a suggestion from Stephane Graber, I tried running:

    echo 3 > /proc/sys/vm/drop_caches

  Which seemed to resolve the problem:

  ubuntu@ethq-build:~/ethq/deb/ethq-0.6.1~git2020517$ stat debian/ethq.install
    File: 'debian/ethq.install'
    Size: 15              Blocks: 8          IO Block: 4096   regular file
  Device: fd01h/64769d    Inode: 7085913     Links: 1
  Access: (0664/-rw-rw-r--)  Uid: ( 1000/  ubuntu)   Gid: ( 1000/  ubuntu)
  Access: 2020-05-17 21:48:36.274528130 +0000
  Modify: 2020-05-17 21:37:17.676232019 +0000
  Change: 2020-05-17 21:37:17.676232019 +0000
   Birth: -
  ubuntu@ethq-build:~/ethq/deb/ethq-0.6.1~git2020517$

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