I'm pretty sure this issue is caused by this mod, but please be aware that I am not sure of all the details I am about to list as we're not able to consistently reproduce the problem on our Dedicated server.

When two ships join using a connector, it's the bigger ship that has the control and the only one that can move - that's how it always was.
However, if the smaller ship disconnects first using their "unlock connector" option while both pilots are in their seats, the bigger ship loses control over the vehicle completely, as if the inputs did not work at all, while the smaller ship is completely fine. Getting out of the seat/cockpit and getting in again does not fix that, even disconnecting and connecting to the server again does not help. Switching the "main cockpit" or "control thrusters/gyros" option on and off with or without re-entering the cockpit did not fix it either.
The only fix we could find is for any other player to enter the "disabled" cockpit - and they can move the ship around normally. When the first player then re-enters their ship, it works normally again too.

This issue also happens when the ship connect through a base - when two ships are connected to a station, two pilots are in their cockpits and the smaller one disconnects first, the bigger one cannot move after disconnecting until somebody else briefly enters his cockpit.

Everything else works for the "disabled" cockpit/seat - switching dampeners, using the toolbar, in one of our trials even a second pilot seat controling a MART turret worked, just not the main cockpit.