Dealers usually don't flash computers unless there is a TSB or an actual issue with the computer. I wouldn't worry about that.

But.... Its possible for them to see the computer is tuned. People argue this, but I was part of the Mustang community (which is huge) and it was proven many times a dealer can tell if a computer has been flash if they intentionally look for it. But with that being said, it took a special visit from an engineer and not something any tech or service advisor could do. Just something to look out for.

Maybe contact LET and ask if they'll flash it again if it gets flashed back?