We are aware the api isn’t optimal to put it mildly. There’s something brewing right now that hopefully leads to a new (and better) api: Technology for new API
The issue with dropping connections is unrelated to that. Applying changes incrementally/more granular without dropping connections is in principal possible, but not the way it is done now. Changing that touches a lot (all?) of sensitive areas internally. And it’s not on the table at the moment.
Right now if you are dealing with such huge deployments, the solution is at the cluster level. There have already been a few discussions on this on the forum. The exact solution depends on your requirements/network topology, but the basics are not to connect every device with every other device, but use e.g. a “hub-and-spoke” topology or something tree-like.