Pitch & Time processing file confusion bug...?

Question

Hi all!
This is my first post. Hope someone can clear this one up!
Having a problem when using the sample window's Pitch & Time processing function. It seems to destructively replace the audio processed with whatever was last on the clipboard. If I'm clever and have saved a copy of the file, I can process again and second time it seems to work fine...
Very odd!

Answer 1

By sample window, I'm assuming you mean the sample editor? 
The Sample Editor works that way because you're specifically altering the original source file.  Here's an excerpt from the Logic Pro manual:
Important: Most edits and functions performed in the Sample Editor are destructive. This means the actual data of audio files is changed. Although you can undo edits and processing commands, you should get into the habit of working on copies of your audio files, rather than the originals. It’s better to be safe than sorry.
So you're spot on in your explanation, that's just how it works. If you're wanting to continue working with your audio files in that manner for Pitch & Time stuff, I'd say keep doing what you're doing by making copies of your audio and working with them like that.  If possible, maybe you could try creating the same effect/changes on your audio within the main arrangement window rather than altering the original audio files themselves, but I don't know what kind of effect you're going for. 
FWIW, the only time I ever use the Sample Editor is to boost or reduce the gain level on an audio file, or to reverse the audio (i.e. reverse cymbal crash for a swell effect, or reverse a long sustained hit on a piano or guitar chord for that cool building reverse sound).