You will get the extra regions. In one of my earlier games (back in 1.1 IIRC), France and GB (myself) were at war. Just before I finished the mission, the 13 colonies took the undefended Acadia, which joined me with the rest a couple turns later.
Also, in my first 1.2 campaign (as GB again), I handed captured territories such as the Iriquois ones, to the 13C (to reduce my admin penalty), and they also joined me again once the mission was complete. A couple were even converted to 100% protestantism...
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