I spoke to Cobb earlier today as I was getting ready to purchase an AP and didn't want to buy a product that potentially wouldn't work with the "new logic" that is supposedly in Subaru's fix. The gentleman I spoke to said that any Accessport flash would simply overwrite whatever Subaru's fix may be, and implied that included any logic changes - he did state he wasn't familiar with the fix though. I didn't ask the second question, that's a good one.
Frankly, I don't understand the revert to stock / divorcing process anyway unless stock in this case means Cobb's stock. My understanding was that the Cobb flash restructured the ECU pretty thoroughly. To revert to true stock, wouldn't you have to have some kind of version control within the flash process that would include archiving the stock programming? Question for a different thread, no need to reply.