Suppose two git-annex symlinks (locked files) point to the same key. If you unlock one symlink, and annex.thin is true, editing the file will change the contents pointed to by the second, supposedly locked, symlink.

Maybe, with annex.thin, when one copy of a file is unlocked, all must be unlocked?

Also, with annex.thin, the invariant that .git/annex/objects/aa/bb/*/* contains content with given key gets broken if the file is edited. Might that affect other things, like metadata lookup? git-annex-fsck reports this as an error.

git-annex-drop succeeds but does not actually drop the file.

Also, even if the current repo is trusted, with annex.thin, an unlocked file should not count as a trusted copy.