What happens if I empty vqcache?

Title pretty well sums it up.

nothin

Do the files come back?

yes. Deleting the cache just means they will regenerate again. You can also just delete the mods.cache file and that will also regenerate the cache files. There is usually no reason to do all this manually tho. vQmod will auto-regenerate the cache files as needed when it detects the xml file or core file that make these files have changed.