Without knowing how Ranger wired your boat, not all are wired the same! You may have two issues going on.
If the thruster battery is the source of power for the windlass then two things to check (1) main thruster fuse 200 amp which should be located near the thruster battery switch. (2) Thruster battery condition , connections, and battery voltage at the thruster itself. With thruster battery switch on check voltage at the thruster battery, the thruster fuse block and then at the thruster the voltages should be close to the same with minimal voltage drop from the length of cable. When checking the thruster battery voltages if you find them to be low put a full charge to the thruster battery and then repeat voltage checks and then thruster operation. Does it work now? Next with thruster battery switch on check the voltage at the windlass breaker located in the head Check voltage at the terminals. If you have voltage at both terminals you have voltage going to the windless. Turn the thruster battery off. Now recheck voltage at the terminals. If there is voltage which I suspect there will be. The thruster battery is not the power source for the windlass. I think the house bank powers the windlass.
When you determine what your voltages are at each component that you are having issues with you can then start to troubleshoot. Without looking at your boat and given the information that you provided I would be looking at two different problems.Thruster - A battery issue, depleted battery, bad connection, fuse open, thruster controller connection or faulty controller, issue with thruster motor or relays. I would inspect in the order listed above because I would bet it will be resolved before you get to the controller. Windlass- You indicated that you heard the relay or solenoid click. This would indicate that the switch is wired to the house bank at the dash and there was power to the solenoids. If you checked the windlass breaker and saw battery voltage on both sides of the breaker and the solenoid is clicking it is time to take a look at the connections at the windlass. Check for voltage at the windlass connections when pushing down on the bow windlass switches. Is there voltage present? (Yes) windlass issue,( No )battery connection issue, wiring issue.
Most of the Fluid motion boats have the windlass powered off the house bank. Personally I think it should be powered of the thruster bank but it isn't on the Cutwaters and I know some Rangers because there was a thread not to long ago that started because when the Ranger owner used his windlass without the engine running it would interrupt his Garmin plotter because of the voltage drop. (Garmin is powered off the house bank)
My theories may be wrong here. So you asked for a suggestion or "Wisdom" I can't give you that!!! Suggestion I can. Troubleshoot each issue separately. They may be related but it is best to start with the thruster, troubleshoot it first.