The prefetch folder should have sort itself out and this is something under the control of the OS.

The entries there aren’t copies of the whole file just location information to speed up loading. I’m surprised if they would have had this impact, now there is a possibility that still being in the prefetch folder they would be looking for the presence of or trying to load these files. In which case I would have expected a windows error ‘couldn’t find file’ or wording to that effect.