Never heard of a E55 engine ECU failure but it can happen and it shouldn't happen. Only strange thing is why this happened after the gearbox ECU unit exchange.
Wait for the new engine ECU unit to arrive from Germany (needs to be programmed especially for your car, may take a few days) and give us some feedback.

Regarding the APS50: at least get the latest software update available. The V 2.1 not only includes new navigational data but also a OS update. Bugs are still there though.

I'll be at AMG in Affalterbach next month, so maybe I can find out more. Unfortunately they're not very willing to give detailled information and the official support for this non-commercial forum has been denied completely.