We accidently shut off one of the isolator valves (thought we were turning it on) for about a day before we knew the pool pump was only on four hours a day because we thought maybe that’s why it wasn’t getting warm. The next couple of days our pool was completely green and has been for a couple days. We also have a check flo light on our Auto Pilot.
If I’m reading this correctly, it sounds like you shut off the flow to your pump, but then allowed the pump to run with no flow for at least a day. If that’s the case then I suspect some damage may have been done to the pump during this time. The pump needs water flowing through it to lubricate and cool it and if it runs for an extended time with no water then it will be damaged.