Megs is down but not out. Using the power of the infused Allspark and pulls himself back together, using bits from the other bots. Maybe he is in stasis lock (if that exists in the bayverse) and Soundwaves scans reawaken him.
soundwave does not send the constructicons to rebuild megatron, their box bios confirm this. i hav eno doubt that soundwave has something to do with it though, as the colouring book says something along the lines of what will soundwave do with all this secret military info.. ie. info on megatrons location