If git-tracked files are removed from the remote, they don't get synced over after a "git annex fsck" and "git annex export".

Is there some way that they could make it to the remote? I'm imagining an rsync-like behavior to copy over files that have different time stamps or file sizes. Would such a feature be welcome in git annex?

Since git-annex 6.20180626, git annex fsck --from an exporttree=yes remote will notice if files on it have been deleted, and then git annex sync --content or git-annex export will re-upload them.

But perhaps more interesting, if the remote is also configured with importtree=yes, git-annex import from it can now notice deletions as well as other changes to the content on the remote, and make a remote tracking branch in git reflecting the changes. You can then merge or revert the changes and export or sync can be used to put the deleted files back on the remote if desired.

Only a subset of remotes support importree, but the fsck method will work for all. So, this is done. --Joey