The controller shouldn't lose the programmed settings, but it's not the first time I have heard about it happening.
Perhaps if the bike shop had spun the wheel fast enough (maybe while checking the chain/gear operation with the new chainwheel) it might be possible that the high voltage generated by the spinning motor could have had something to do with it.
Put the settings back where you had them before and wait and see if it happens again. If it does, then the controller might have to be replaced to cure the problem.
Alan