Wow, its not just me 
I spent 3 hours with a couple of clients tuning a vocal performance in vari-audio. Then when finished I went to add a process in the offline editor. Boom, suddenly all of my vari-audio tweeks were gone. Luckily I had not saved between the two processes so I was able to re-open the past version and my tuning edits were still there.
But as Fabietto says, if you do absolutely anything to a file once its been vari-audioed, it will re-scan and you will loose your tweaks.