TED LECKIE  The best way to get something like this fixed or if you are having trouble is to contact us directly at ironicfeedback@mac.com. We answer all our emails and can usually figure out what the problem is pretty quickly. MacUpdate, great as it is, is not really a support forum.  
(Version 1.5.2)

TED LECKIE  Hi Dean, I've tried to contact you but couldn't find you in our database of users who have bought Yep so if you would be so kind as to email me (our email address is on our contact page at yepthat.com) I would appreciate it. Yep won't move files on its own (there's just no code in the app to do such a thing!) and certainly won't delete files. So I'm curious about your experience, whether it is some confusion with the UI or what. But the only way to get this sort of stuff improved (or fixed, if need be) is to email us so we can start a dialogue and figure out what happened. Thanks,

Ted  
(Version 1.5)

TED LECKIE  Yep doesn't move any of your PDFs (or at least it certainly shouldn't and if it has then we definitely want to hear about it. Our email is on the contact page of our website). You can change where Yep looks for PDFs through Yep's Tracking prefs. It's probably best to think of Yep as a very specialized Finder for PDFs.  
(Version 1.5)