Geothermal system repair gone wrong

We had one simple dripping Taco valve on our geothermal. The system ran both ac and heat without issue. We just had to catch the slow drip in a bucket. We had a certified geothermal repair team out who told us it was not to code any longer and they proposed some repiping and two new valves, one for each handler. It was installed in 2008 so it could be accurate that updates were needed. We agreed. Cost was around $$$$. First set of valves was not correct, so they came back out. Two different looking valves were fitted and we were assured they were better than what we had originally. They turned the units back on. That's where the trouble started. After doing the repair and adding two new valves, they turned the system back on but did not turn the geothermal pump back on first. It was shut off during the repair. So it ran for perhaps 24 hours with no main geothermal pump on. It was not checked obviously or they would have seen it was merely blowing room temperature air. No one ever checked the air temperature at the registers, and they didn't even go back to where the well pump was. We even reminded them the pump was off. We had them back out and now they tell us there are blown areas on both circuit boards. They site the age as the reason for this, but all was running perfectly fine before these "upgrades" and new valves. What impact does running a system without the pump have on the units? Is there a procedure for turning the geothermal well pump back on after it had been shut down? The first set of valves they put on did not work so the well pump cycled on and off constantly not keeping pressure for a few hours before we figured out something had to be wrong and called them. It's all very frustrating.