By pass all the limit switches and relays going directly to the flap motor leads with a external battery (drill motor) to get the flaps back into the usable range.Then verify the wiring of the limit switch and the relays along with the flap switch itself. Also verify that  the limit switch is operational. The only way the flap motor will go beyond the limit switch is if it's failed or miswired.

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Jon Hadlich
AI Systems
(541) 815-7381