A lot of the movie people wanted them separate too. Joss didn't want to use Coulson for example, because he said that in his mind he is still dead. I think SHIELD was still planning to pretend to be in the movie universe until post snap, right?
They like kind of mentioned something happening in wakanda but never mentioned anyone disappearing? That's what I gather, but I never watched the last 2 season of AOS so I don't know for sure.
AoS is still in the MCU (Fiege can have it when he pries it from my cold dead hand). The last episodes of season 5 happen simultaneously with Endgame and end before the blip, seasons 6 and 7 happen 1 year into the blip (with an epilogue 2 years into the blip). They're lucky in that the main characters didn't blip, and don't mention it but they are a year into it and busy with 3 simultaneous alien invasions and quantum realm time travel (that eventually leads to an alternate timeline hop, but they return).