If I use F-k and the directory contains Emacs backup files (*~), I get an error message about the directory/folder not being empty. I assume this message is coming from rmf, but I haven't checked. Since MH-E provides a way to edit messages, MH-E should just automatically remove these backup files before trying to remove the folder.
Or I suppose we could add a folder-pre-kill hook, so that the user can make the deletion happen automatically.
Back in October (2021), there was a question on mh-e-users, asking why each invocation of "F n" in a folder was producing a new, numbered unseen sequence folder in +mhe-search, rather than just reusing +mhe-search/sequence/unseen. The problem wasn't readily reproducible, so we never got to root cause.
I have now seen the problem a couple times. In each case, there is an Emacs backup file (and no other files) in the directory for +mhe-search/sequence/unseen.