If it's cycling the pump much, you probably don't want to allow that to continue. On/off duty is hard on a lot of things, including motors.
Otherwise, I know nothing specific about the Pool Pilot. I assume you've found the manual, and gone through the trouble shooting process there? If that didn't help, and power-cycling the control panel -- ALL power to the electronics off -- didn't restore it, I think you'll need to call the mfg or a service guy.
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