I think he left and came back. For a long time, I just stopped seeing him in their performances and appearances. The last I saw, he was performing with them again. I don't know his whole story, but according to Jaguar, they always treated him as the stand-in nikka. She said he started as the stand-in nikka for Scott Storch, and now he's the stand-in nikka for James Poyser. It makes sense, tbh. On another note, I wonder what happened to the bass player from back in the day who always had the chew stick...
EDIT: From Wikipedia... Kamal Gray did not play with the Roots on Late Night With Jimmy Fallon between April or May and early September 2012. His absence was not publicly explained, however on the September 17, 2012 (NBC's 'Late Night' 700th) episode, Gray returned to the group.
I coulda sworn it was longer than that (like maybe a year or two), but I knew I remembered an absence. They still be keeping his ass wayyy in the background, though. Although Kamal has been with them from the 90s, I can understand why they brought in James as the main keyboardist. A Tonight Show type of gig requires the most polished musicians. That's not to shyt on the brother Kamal, but James Poyser is James fukking Poyser.