My handheld seems to be working fine....I've loaded a couple tunes since the dealership flash. The handheld loads the tune....no errors or messages on the handheldIf the dealer flashed over your tune, your handheld programmer should be useless unless you pay to have it unlocked.
I don't think the dealership screwed up your ECM. The problem is you didn't flash back to stock so your handheld programmer is now locked.
Any good tuner can help you out, you'll just upload the stock tune and send it to them. Definitely use EOC.