I think the most annoying issue is that you can't actually rename a folder in the files tab of the project (this could be so easy!). I generally go to the files tab, select everything in the current folder, right click -> Move on disk..., create a new folder at the desired destination and press save. As this entirely depends on LabVIEW, there is no relinking done (well there is, but no search dialog). However the old and now empty folder (including the entire filder hierarchy) remains and cannot be removed because LabVIEW keeps locking it (I think it is the search location for the next save/load dialog).