Well, the temporary files are in the standard Windows temp folder (under User/Appdata), but there should be nothing deleting them if they're still in use. At a minimum, PI should be ensuring the files are locked while it's using them so that CAN'T happen. I've never had any other application have a problem like this though, and I regularly leave things running for months. There's no reason PI should be having this problem other than that there's a bug in PI.
At any rate, I've gone ahead and moved pointed PI to its own temp folder so we'll see if the problem recurs.
Beo