I think we're over-complicating things, here.

New Year's Eve, Cuba. That's when Fredo thought he was gonna get whacked. So he does what anyone, stupid or smart, would do. He runs. Mike gets home and sends out the word to Fredo that everything is OK. Fredo believes him. Then, after the Senate hearings. Fredo is exiled and living elsewhere. After mama's death, there seems to be a reconcilliation between the brothers, and Fredo returns and lives at the Lake Tahoe Compound.

Why in heaven's name would he come back and live with his brother if he thought Mike was going to kill him? Fredo was stupid, but not that stupid. Clearly,he thought everything was OK between the two of them. If he thought Mike was out to kill him, he was certainly smart enough to head for the hills, just as he did in Cuba.

Fredo, I believe, had no idea he was about to die, either on the boat or any other time.