It sounds like tfpt online
is detecting that the folders have been deleted. It is trying to pend a delete on those folders, but it sounds like you have already pended different changes on the files within those folders.
tfpt online
will not pend a deletion of the folders if you have other changes pended for its children.
If you want to delete the folders, undo the pending changes on their children, make sure that the contents on-disk match what you want, then re-run tfpt online
.