The tree generated by git-annex sync with a borg remote does not seem to get grafted into the git-annex branch, so would be subject to being lost to GC.

Is this a general problem affecting importtree too?

Yes, it was. It would have only caused a problem if the user kept doing imports from a remote, but never exporting to it. Then, in a clone of the repo that was importing, they would not be able to get files. fixed --Joey