I think I see what's going on. Ecryptfs copies up attributes from the
lower filesystem's inode directly. However the practice of overlayfs is
to only copy up i_uid, i_gid, and i_mode from the lower inode into the
overlayfs inode, and to fetch other attributes from the lower inode on
getattr.

The pattern I'm seeing is that inodes that overlayfs has "copied up"
from the lowerdir to the upperdir show up okay. I suspect then that it's
the vfs updating the timestamps in the overlayfs inodes whenever the
event happens that triggered the copy-up.

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https://bugs.launchpad.net/bugs/1636890

Title:
  invalid file times with overlayroot and encrypted home

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