I have been owning both for quite some time. I do remember that outside the Brotherhood Sanctuary they used to appear together. Then I obviously kept using Shadowmere and I didn't track what happened to Frost. Now I am not sure if Shadowmere is dead. It shouldn't. As fas as I remember I always checked that it was alive and I am quite sure the last time I saw it wasn't before a big fight. The fact is that after jumping from a city to another I went into the open space and I couldn't find it anymore. I assume it is yet another bug.
Any chance to get Shadowmere back? All other horses are just useless. They die after a small jump (I mean, quite small). I knew since Oblivion that it was supposed to be immortal, and so it should respawn. The problem is where. I checked both sanctuaries and it wasn't there. Unless I had to wait few extra days.