Playing on an Enigmatica 2 server and I had flux points connected to all my IC2 machines. Logged in today and they are all floating in front of the machines disconnected and I cannot get them to reconnect no matter what I do.

Flux points can only connect to IC2 cables or energy storages (MFSU etc). And only plugs can receive energy from cables. Because they're not a part of IC2 energy network, you can use mekanism cables temporarily. I'm not likely to support for it.