as long as they didn't change the redline you should be fine. most dealers flash you back to stock with the latest ECU "fix" after any service. unless you report an issue with the engine they aren't going to hunt for a tune. I wouldn't worry about, just don't tell them.
2008 M3 Sedan + catless + Tune
2012 CLS63 AMG
2014 M6 Coupe + catless + KW V3
2015 Porsche GT3