It's going to come down to your dealer. And if you keep using the same dealer they can tell it's been flashed as the ECU reports a write count. So if they saw 3 writes when they serviced it and the count goes up next time, they know someone did it other than them. Whether they care is another matter. My Triumph dealer is great. I talked to them about loading the tune, and they admitted that Triumph would have to prove the tune caused the issue to deny a warranty claim. But any drive train issue they'd point to it most likely.
Anyway I put it in for service last week and when I picked it up they were like "Your bike has a tune, right? We flashed the ECU again as there is a new version, and flashed the BT module as well. We aren't sure if it overwrites the custom tune throttle maps, so see how it rides, you may have to apply it again..." Not bad for a Triumph dealer in my opinion!