I don't see why he has to choose between them, but at this point I would definitely give Sanctuary the priority and let NM take the back seat. The other two left to play shredcore and instrumental guitar god albums in an attempt to show their ass to the rest of the band, only it backfired with dismal receptions and sales. Nevermore wasn't Metallica; there is no James Hetfield telling Jason Newsted that he can't do a side project, and if he does he'll be fired. They took it upon themselves to leave behind a great band with their delusions of grandeur, so at this point it doesn't really matter anyway. Also, Loomis' riffs on his solo project were better than the last NM album, which begs the question whether or not he gave a shit about NM in the last couple of years in the band due to the disappointing Obsidian Conspiracy.
I just listened to the new Sanctuary and it's head and shoulders above anything since EoR. Warrel is 2 for 2 now. If the other two were smart, they'd cut their losses, swallow their pride, and admit that Warrel is the glue that holds the band together and beg to start SERIOUSLY writing a new NM album. Also, drop the fucking seven string.