my take is they probably back to their "eorzea" body state but will keep their "SHB" mental state. so physically they will be back to pre "transfer" but their mental/mind state is still up to date to current event.

i mean its kinda convenient at this point, when SHB story is done and expansion is announced (among with new class), if the scion really make it back to their bodies then yoshi could just slap the new class to the scions under context that the scions has learn a lot of things over there and they decide "class up" their old body, and later portray them in full glory in CG trailer in the future.

i can see it, CG start with the scions waking up one by one then as time move on we see each scions start training their body back and glamoring new clothes and new class.