@blanchsb This should be possible with a “UV Map” node in your Cycles node setup for texture baking in order to specify a different “UV Map” than the one you used for symmetrical texture painting. And the new “UV Map” should be the one from unwrapping after the application of the “Mirror Modifier”. But I’ve to try it out whether it works like this.
A propos “Normal Maps” and “UVs”: I’ve seen recently this video from @jlampel about “Normal Maps” and sharp mesh edges.