It should be possible for this to work:

joey@darkstar:~/tmp/bench3/a>git annex move x --from d
move x (from d...)
  dropping content from an export is not supported; use `git annex export` to export a tree that lacks the files you want to remove

git-annex could just alter the tree exported to the remote to remove the file. It might be a little slow to do that for a lot of files, and it would create some unattached tree objects that would linger until gc.

A simple optimisation would be to remove the file (with removeExport) but not update the export tree for one file. Keep a log of removed files, and at the end of the command, or some future point where the export tree is used, update the export tree to remove the files from it.

This seems like a prerequisite for remove legacy import directory interface because git-annex import --deduplicate and --clean-duplicates need to remove individual files from the remote.

Note that doing this with an importtree=yes remote would result, after import, in the remote tracking branch having the file deleted. That could be surprising when merged, since it would delete the file from master!

I think this problem can be avoided by rewriting the remote tracking branch's previous commit to not include the file that got deleted. Then merging would need --allow-unrelated-histories, but would not cause the file to be deleted from master.