How will this effect the Netflix shows?

It'll most likely affect Agents of S.H.I.E.L.D in some way like a few of the events from the movies. It's always been more reactive in that regards. I think the Netflix series will continue like they have with maybe a very vague reference but I feel like they exist in their own bubble, so they won't impact it much. It's most likely too late to effect all the NF shows between now and Avengers 4.