There are very few ships being removed from the mod. Quite a few are getting replaced. As for ships that go from being open-use to closed; the v4.85 IMG line is going to the CR (and the IMG get new ships as compensation). The Falcata is going to the Outcasts, but we get the Cutlass Borderworlds Bomber as the open-use BW bomber.
Ships for the Reapers of Sirius, of course, are only open the RoS. Phantom stuff is still closed.
I don't know about the Zoner Carrier or Juggernaut. I didn't think they were going to be closed.
The Spyglass Battleship is going back to being restricted to the Hellfire Legion (I'm not sure if the Vagrant Raiders get to keep their Spyglass or not.)
Edit: PS: If you have an indie Lane Hacker Spyglass, your chances of keeping it are somewhere between zero and impossible. Just saying.