I think you should be fine separating them. Once they get settled, you shouldn't have any trouble. Your biggest issue would be trailering just one (I'm assuming your brother's place is too far to walk
). With our buddy sour horses, when we would trailer one, both horses would come out to the trailer, the one who was leaving would be loaded and tied, then, once the door was shut and the truck ready to roll, the horse who was staying behind would be calmly but purposefully returned to his stall with a pile of hay and a bite of grain to keep him occupied. If he chose to be quiet, great. The first whinny got him a dark barn with the windows closed and no human company until he was calm. Both horses usually calmed down quickly when they were too far apart to hear each other. A more permanent separation (ours were only for single day shows) might be more successful over time, though. If you each have other horses, the newly separated ones should relax and "assimilate" into their new herds pretty quickly. We only had 2, so they became attached at the hip within weeks.
I hope that helped! Good luck!