Apparently so. Some kind of "deep record" in the ECM. Nobody ever used to look for it, but since the big EPA chitfest with Harley and the "race tuners" the MOCO reps now go looking for it !
In the past , if you flashed back to stock using TTS , the local dealer would "see" a stock calibration and would not dig any further , changed days today I hear.
As far as I am aware the Supertuner Pro NEVER had the ability to do a stock reflash , it was always a one way one direction trip kinda thing.
Some say TTS still flashes back to 100% stock OEM , but I'm sure that's a risk for "warranty". ( PLEASE CORRECT ME IF I'M WRONG HERE FOLKS , I'M ACTUALLY HOPING SO !)
Now I just sold my "out of warranty" 2013 CVO Breakout ( Supertuner Pro ) , and have just the one bike , a 2008 CVO Springer ( "original" up to 2008 SERT AND "early" TTS).
MOCO can do "sweet fork all" to either of those bikes now thankfully , but if you're still under warranty be careful is the word !