[...] all folders and files in the work folder can be deleted

Yes, but be sure to quit Sweet Home 3D first.

HawkDawg, thanks for proposing a file that shows this issue. I've got already one but yours might reveal something else...

mazoola, thanks for your patience to search a way to reproduce this issue. I don't think that saving the .recovery and .sh3d files at the same time is a problem, because the tasks that handle these operations work on copies of the edited home, so they don't share any data.