So for some reason my Pentair EasyTouch system creates its own pool schedule from 8-2pm. I don't know why it does this but I keep deleting it and it keeps recreating it. I have talked to my poolman and he says he is not doing it.
Modifying the schedule using the handheld will change it directly on the outdoor unit. Any scheduling changes are saved to the outdoor unit regardless of whether it's done on an indoor or wireless remote... a remote can't even see schedule information unless it's connected to the outdoor unit.
Clearing the eeprom on a remote only clears the programming (settings/schedule/etc) on the remote - it doesn't affect the outdoor unit. If you want to clear the outdoor eeprom you have to do it at the outdoor unit. At power-up, a cleared or 'blank' controller - indoor or outdoor - will 'sync' and grab programming from another connected controller.