folded $6000 pot for $400 on river.

[Forbillz]

I think the thing to consider is not whether he had the flush, but what's in his head? Hindsight says this:

I'm going to call this guy with my middle set anyways, so I'll slightly increase my equity by being the bettor, not the caller.

And it worked out that he increased his equity more than he thought, since you folded.