My idea is to decouple a lander from the main ship, and then dock back up after, but dock backwards just because it's easier to place the docking ports that way. To stop the mothership being despawned, I put a probe core on it.
That much works fine, but afterwards, I can't control. WASD have no effect. If I turn on RCS, and I ensure the command pod is Control Port: Reversed and the probe core was on default, then I could control, at the cost of using monopropellant.
If I turn RCS off but turn SAS on and select options like prograde and retrograde, it will use the reaction wheels to successfully point that way.
Does anyone know what's up with that?
You have docking mode enabled, rather than flight mode.
Docking mode allows you to have granular control over the RCS thrusters and disables the main engines, because pressing SHIFT would send you smashing into the docking port at 40 m/s.
Check the bottom left panel.