Much depends on what year model you have. They're not all the same. We have a 2008 25 classic. On our boat there is a breaker under the vee berth on the port side. The power comes off of the power supply to the thruster. So yes I suspect it's no coincident that this happened after thruster work. The terminals for the thruster and windlass are located all the way forward under the access hatch under the berth. Power for the windlass runs from the common terminal with the thruster, back to the breaker under the port side berth, then on back to the solenoid behind the helm panel. Then from the solenoid back forward under the starboard side gun'l cap to the windlass.
I'd check the breaker and if that doesn't fix it check to see if they neglected to re-land the windlass power cable when they worked on the thruster.