Depends on the dealer and what it's at the dealer for, if it's a non drivetrain problem then it shouldn't be a problem, however if it's in for a drivetrain problem you can always return the ECM to stock before it goes in.
It's not a bad idea to return to stock anyway as I've heard of a couple of guys having problems when the dealer has flashed the ECM to update it to a new version even when it was in for a non ECM issue, this will wipe out your programmer tune, then if you try and change something with the programmer it will be locked and have to be unlocked by the programmer mfg.
2013 JKU Rubicon - Commando and 71 Jeep CJ5 (pretty much stock)
Teraflex 2.5" spring lift, Teraflex monster front and rear trackbars, G2 wheel adapters, Goodyear Wrangler MTR Kevlar 35 x 12.5 x 17, Superchips Flashcal, Warn Zeon 10, Smittybilt XRC bumpers front and rear with tire carrier, Metal Cloak Overland Fenders, Uniden Bearcat 980, Homemade side rails. 50" and 20" light bars and brackets.