Well, let's see if I can help...
The ECU's flash memory threshold is estimated at about 100 flashed before it's burnt and un-usable. That's a lot of flashes, IMO. With the AP, you flash a base map, which ever base map you choose, and that's the only time you will flash your ECU. The "real time" maps are maps that are run ON the ECU, but not stored inside. I like to think of it in terms of volatile and non-volatile RAM.. (sp?) The real time map is run till you take it off, or your ECU has been hard-reset (disconnect battery). Then it reverts back to whatever the last base map was being used.
As far as the dealership knowing, I'm not sure. BUT, before you take the car in for any thing, just Re-flash the ECU back to Stock-Mode using the base map COBB provides.
Hope that helps, but it probably won't since I suck at explaining stuff.