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Here lately I've noticed myself checking the river against busted flush draws headsup especially when I have marginal holdings.

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I think the fact that the flop is paired here is more important then there is a busted flush draw.

You played this hand fine.

When it comes to making the check/bet decision on the river when its been checked to you HU with a marginal hand you just need to ask yourself "Is he calling my bet here with hands I beat more often then he is calling/raising me with hands I lose to?"