things are really simple, no hidden bits or bytes

How i would do it:
The flash counter is updated on the PC software side and transferred to the ROM

so in rough lines it would work like this:

each rom will have its "license", database kept on the PC.
flash procedure starts
-check "licence"
-read flash counter from ROM
-compare against counter stored in PC database, PC database ALWAYS has correct number so you cant fiddle with it
-increase counter
-rom file update
-physical flash

rinse & repeat

 

I am over 2500 now and going strong. I stopped counting to be perfectly honest so it might be over 3000. Alot at any rate.

 

Tiny - this isn't the ECU keeping track of the number of flashes its the software.

anyways ECUTek might do this - but who cares, ECUTek is a rip and noone uses it anymore...

 

yep, thats what i am saying
There could be a possibility that the ecu keeps track of flashes, for example the actual kernel that does the comms/flashing has a simple code fragment to update a counter.
In any case, if the OEM manufacturer wants to do it, they most certainly can do it.