Glad you pinpointed the problem so now you won't have to reinstall.
Looks like your persistence paid off.
If you're referring to the main XP Prefetch folder, you can delete the tiny .pf or not. It doesn't really matter as windows will automatically control the folder contents (assuming default registry settings). You can also use a tool like NirSoft's WinPrefetchView, but again--you'll actually be micro-managing an area where XP auto-manages just fine.