Bubbles's chassis may have supported far more lethal weapons than her mere bulk and strength (!) which have been removed - just as removing Pintsize's laser was considered sufficient.
That is undoubtedly true, but still, the great size and strength of her current chassis is still enough that I imagine the military may have wanted to take it back.
So it could be that:
1) Bubbles was allowed to keep the chassis as sign of respect for her loyal service
2) With her PTSD, it would possibly have made her personality much worse if forced into 'downgraded' chassis. Who knows what she may have done
3) There may be a law making forced abandonment of a chassis illegal (although this did not stop Turing from trying to repossess Pintsize's chassis)
4) Instead of the chassis optimized to Bubbles' AI (as OldGoat suggested), it may be that AIs, after spending a certain amount of time in a chassis, are adapted to such an extent that forcing the AI into a different chassis is bound to be unsuccessful. Only voluntary chassis change would work then (e.g. Winslow)
5) As Dave H suggested, military wanted to keep the option of recalling her. Not sure about this, because they likely could've simply uploaded her back into the military chassis when her service was needed again
I like the 1st option best, so in my head that will be canon