Somewhat late Chime in from Australia
Well yes , the Supertuner pro IS now locked to your bike even tho' the bike already had a TTS tune.
I have seen the exact same scenario here in Australia. Dealer tried to load up a stage 4 tune to a mate's Streetglide in 2012 that already had a TTS tune.
They did not tell him they were gunna AND he did not tell them it already had TTS kinda sad story. PLUS nobody knew that TTS "locked out" any other ECM access at the time.
SO the bike had to get an "Unlock" TTS cal from TTS ( easy enough to get from TTS online but still a royal pain in the ass truth be told !)
You can get the Pro dongle unlocked in Australia and Europe , ( and prolly the US now as well) but more $ spend.)
BUT as you don't have the TTS dongle that is not the way to go. You will have to "borrow" a TTS dongle and put an "unlock" calibration into the bike to let the Pro software communicate.
(AND yes mate dongles "go missing" in Australia ALL THE TIME , such is human nature, Sitting on a garage shelf and the bike has changed hands 3 times etc etc)
THEN the brand new Supertuner pro would reflash the bike. A bit of a "journey" , but perhaps you are there already ?