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Try disconnecting the battery and holding the cables together for a while. This will discharge the capacitors that hold power and memory even when the battery in not connected.
Troubleshooting:The engine does not start and LED remains off. 1. Check PATS system fuses 2. If alarm is fitted check if LED functions for alarm: if not check cigar lighter fuse (also used for LED) 3. If not go to main dealerEngine does not start: LED flashes rapidly Leave ignition on until the LED starts to flash a 2 digit code: (sequence- pause-sequence) Check the following codes: Code flashes: 1:3 Key code not received. Is key screened by other keys or objects? Try different key: if okay then first key is faulty. If not go to main dealer 1:4 Partial code only received. Try again. If not okay use different key. If not go to main dealer 1:5 Key not programmed into PATS. Program key as above using master 1:6 Faulty link between PATS module and EECV Go to dealer .For more information and troubleshooting tips:PATS-Troubleshooting-DIAGNOSTIC-Service-Tips and:Programming Ford-PATS
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You may need to tow to dealer, or you may be able to call a mobile locksmith who has the correct Ford software. You will need to get the code, this will be needed to diagnose any farther. You need a dealer scan tool, or high end snap on or similar.