Depending on how your model is made, you might actually want to keep it exploded for the AO bake. For example if you have floaters on one side of your symmetrical model with mirrored UV's, you'll be baking the AO on both sides instead of one. Have a look at the polycount wiki for some examples…
If you bake it in 3dsmax you can define Materialid's for the lowpoly and highpoly and check in the bakingsettings to hit only the matching ID's. This way only for example faces with material ID 3 in the LP will get only hp information from the highpoly with matid3 in range. I wish this option was possible in xnormal