in terms of K04 cars which the 35 is there is a big difference in feel between a Stage 1 and 2 car, quote my wife today, blimey your car is loud
i suggest you decide what you actually want to do with the car as this will dictate the order you do things, if you add and exhaust and just a catback you will be still at Stage 1
On the flash counter front decent mappers can reset this to what the number is on these engines, on the EA888 in the TSI GTI Bluefin increases the flash counter everytime you use the handset, it does not on the K04 cars due to ECU type, they were economical with the truth on this and Revo pointed out mine was at 7.
APR and Revo stock maps are not the oem one, Bluefin does put your original map on, if you are really worried with APR and Revo their dealers will ref lash the oem file for a nominal charge
don't touch the APR intake on a K04 car you are just wasting your money
when my car was serviced i had it flashed back to standard by Revo (my dealer asked on that occasion to make life easier as mine is the only 35 they deal with), car did not have an intake but they were relaxed about the other hardware as that is at their discretion
if you have warranty worries don't map it