With the last Marvel's Agents of SHIELD ending with a bang thanks to Eli Morrow, the fate of Phil Coulson, Leo Fitz and Robbie Reyes is a bit up in the air. Would the series kill off two long run characters and one they just brought in? Probably not. But actor Clark Gregg told EW.com:
The more sophisticated audience members will suspect that Coulson may not be dead in episode 6 of season 4, and probably the same goes for Fitz and young Robbie Reyes.
So we don't know what happened to them and won't know until November 29th… it seems safe to assume they'll be back.