I created a local annex directory that's an adjusted branch used with the assistant. On another machine, I initialized an annex directory, then made this into a full-backup ssh remote for my local.

After the assistant pushes to the remote, and the remote runs git annex sync, the remote is missing some directories and has some extra directories. For example, it has the extra directory Documents/programs/Documents/programs/, which has different contents than Documents/programs/. Both directories are missing the subdirectory graphing_experiments/.

From my local, git annex whereis Documents/programs/graphing_experiments says the directory exists on the remote. But it's not there.

I recreated the remote from scratch and the problem persists.

The assistant says the remote is caught up, and is keeping up with new content changes. What could cause this?