Agreed with the previous comments. They can't tell if you've tuned the car if you unpair it first, only that it's been reset recently.
When I took my Focus ST in for repair they asked about the reflash and I said "my mechanic reset the computer thing to try and clear the error code, wuts a tuner?" Then the service tech proceeded to explain to me what tuning was and I said it sounded interesting, and that I should have my car tuned.
Anyway, they could not figure out how to turn off the CEL so the whole ECU was replaced under warranty. They sent the ECU back to Ford to figure out what was wrong and that was the last I've heard of it.
Also, if you keep the tune on and they update the software not knowing the car is tuned, it could potentially brick your ECU. So always unpair it anytime you take it to a dealer. Even if it's for something unrelated, since they might update the ECU out of courtesy.