It shouldnt have caused any damage to the engine while he was trying to start the car with the AFM the other way around.
The engine light will be coming on and off regularly because his car isnt tuned for the different intake. Exact same thing happened when i put on my AEM intake regarding the engine light, but my car never ran/idled rough or shut itself off. Also, i put the AFM on the right way around :P

If your mates car is gonna be running like that with the intake on, i suggest to change his intake back to the stock airbox and add the cold air when he gets a tune. Much more likely to cause engine damage by running that intake on the car without a tune (as it would be running more lean) than trying to start the car with the AFM backwards.

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"Wrong fitment".