Carbon dosing would only be effective if you were running your skimmer. This might help, but as others have pointed out, it's possible the skimming could remove a portion of the medication. If you are carbon dosing, I suggest continuing so the bacterial population doesn't crash, however if you remove your skimmer, you won't be lowering your phosphate/nitrate during treatment.
Given how much a PITA bryopsis can be, my viewpoint is that bryopsis takes priority and if I have to do a couple more water changes after treatment to lower my nutrient levels, that's a fraction of the work I would have put towards battling the bryopsis

. Sometimes you can't hit two birds with one stone, but given the magic bullet fluconazole has been, who's complaining