TT - I don't normally like to disagree with you mate but on this occasion I think I may have to.
The flash counter can be viewed with VCDS - Look in Advinced ID of Engine 01.
The flash counter can be 'reset', I know for sure REVO do it I've seen it with my very own little peepers.
The Checksum is also dealt with by the software, it would have to be because as you quite rightly say if the ECU sees a change in the checksum it will lock up tighter than Phil McC's wallet!!