I'm sure they can figure it out, whats the chances of the dealer sending the ECM to HD.....
My questions is: If I have come of these 110 problems people have been having and the ECM has been changed, is HD going to give me chit about it?
Am I safer with a SERT rather than a TTS or another programer?
You can run upload either the TTS or SERT tuning files, so if you have concern that HD will detect a TTS file, then upload a SERT before service or warranty work. If you stayed with MT6 tuning files, i don't think the dealer could tell if you were running TTS or SERT, thats a good questions for Steve.
In 2006 i had broke down on the road (my 110 blew up) near Fresno. I had a DTT ignition on it at the time. I got towed into Fresno HD and they would not touch the bike because of the DTT ignition. I ended up towing to to my dealer in Yuba City, changing the ignition back to stock first. My dealer then did the necessary warranty work on it no questions asked. It's hard to say what one dealer will do, versus another when it comes to warranty work when you have performance parts installed. Your best changes are to stay with your local dealer and let them do all the mod and service work.
I just recently threw the towel in and voided any chances of future warranties. I installed a Jim's 131 and currently breaking it in,, and so far loving every minute of it.

My dealer is aware of this, and they did not waste a minute letting me know i no longer have any warranty. I've got issues with my gas gauge not working, and we will see what they do about this, which has nothing to do with the motor swap. I can understand them denying drive train related problems, but anything else, they better cover.