Cool...thanks for that info!! So, I should have no problem trying my new baffles, and seeing how she runs, they won't have a clue?
I figure it can only help her breathe better
But I needed to know how much they can " see" with the bikes computer. by the sond's of it....nothing like that 
Please excuse me for intruding and actually posting on-topic info, but I have been unable to confirm how much info the ECM actually retains. I have seen reference to other aftermarket ECMs, namely Daytona Twin-Tek and Zippers Thundermax that actually store time spent at different throttle or RPM settings. I haven't been able to confirm if the HD ecm does the same.
I asked a service tech if I could bring in my bike and have them provide me with hours and info like that, and was told NO. Maybe not, but it seems too easy to collect. Maybe it is more super secret info for internal use only.
But more directly to your question, there is no way the stock ECM can tell what modifications you make to your bike, unless those mods directly interface electrically with the ECM, and then it is still questionable.
SERT definitely leaves a footprint. Power commander - the jury's still out on that one.
Enjoy your bike,
Chief