True enough there, it does seem unlikely, and your solution sounds like a sensible one.

Being that badly damaged would also give another reason why they end up in Autobot custody to start with - if they are so badly damaged they'd need to be totally transferred to new frames, Megatron may have left them behind because such a transfer is too costly on Decepticon resources.
The Autobots? Soft-sparked fools that they'd do something so extensive for enemies... but in this case, there's extenuating reasons why (going back to the whole point of the Seekers being younglings in adult frames).