If you blueprint an existing setup with requester/provider stuff into a new blank spot, bots will build them properly and will keep the configuration. However if you paste a blueprint over an already existing setup, the IN chests don't update with the new information. Imagine that you have a defensive wall with turrets with a lower tier ammo that is far away from you and you wanna update the ammo for those turrets with a blueprint, it won't work.

Last time I tried fixing this bug, the Factorio API doesn't expose a way to detect when pasting over an existing entity so unfortunately I don't think this is possible. I'll definitely take another look though when I next work on the blueprint code.

Maybe you would need to temporarily define some of the chests in the blueprint as requesters and some as providers, since IN chests are both (kinda like buffer chests, maybe could be an angle) then maybe that could work... Probably the Warehouses mod or Angel's Warehouses could help with that or SpaceExploration from Earendel which has a structure that sends items across surfaces kinda like IN and can be blueprinted.

temporary workaround for those with the same issue:
Make a decon planner with IN chest in it, box around your constructed setup (contents will be tossed in the network, no worries) then paste the blueprint above it.

Until there's a prettier way of doing it, the above works.

Thanks for the workaround! If I have the time I'll take a look at space elevators and/or warehouses to see if there's a technique I can borrow for Network Chests.