If you try to delete a file with annotations, you are now shown a warning that annotations exist along with instructions on replacing the file, if that was your intent.
If you are subscribed to Music Stand, your team members can add annotations to PDF files with their personal notes. If you have an update to that file, you can replace it by dragging the new version onto the existing one. If you don't know that, you might try to delete the existing file first and then upload a new one, but that will also delete your team members' annotations. The new warning should help prevent that.