If he returned to his original body and magic power didn't get returned, they are in big trouble.
The magic transfer is the origin of the soul exchange, and it's strange that it was maintained when time was reversed. So I would expect that the soul and magic will get back to their rightful bodies, though as you say, that might be an issue.
It'd be the worst for Gideon if his soul returned to his own body while the magic followed the prince's soul...
Please let that be the actual prince with the OG Gideon rotting in a ditch somewhere.
Or maybe down the road OG Gideon back in Gideon's original body will be reunited with the Saintess of this reiteration that is obsessed with Gideon.
Considering that Gideon's body was definitely the target of an attack, I expect he isn't in a good condition, possibly disfigured.
But hey, the Saintess could do something about that and likely will because part of her sentence is working at the hospital to heal people and healing the person who contributed to the war is inevitable once he's found alive. The prince knows where Gideon's body is located so they should find him.
As you say, Gideon could get his happy ending; the saintess was interested in him this time around, she heals him, he asks the king to give him the saintess in marriage as a reward and to pardon her and maybe the saintess is grateful to him and actually loves him (well that's the part of the plan that's likely to fail, but you know).