ATTENTION: POTENTIAL SPOILER AHEAD!
In the end Perico (the uncle) plays a secret recording (he got from his FBI informant) to his nephew Skunk to show him that Moe is really an undercover cop.
When Moe is brought back in and Skunk is about to kill him, he kills his uncle Perico and his men instead and doesn't confront Moe with his knowledge about him being an undercover cop, but instead that his uncle wanted him dead because he was a potential threat to them.
Has Skunk done this to protect Moe so they can stay friends?
That would be very risky, because if Moe recovers from his amnesia he might turn in Skunk for good.
It looks more like Skunk was the undercover cop from the beginning and the FBI just misinterpreted the evidence (secret recording).
Who was the undercover cop? Moe or Skunk?