My contractor is installing a tub in the basement and he but cement boards all over except right behind the tub it is up against the studs. He put cement boards on top of the tub over the flap. Is this OK?

Yes

Chuck

It's not OK to run the board down over the flange, that'll make the board bow inwards. Either apply shims on the studs or stop the board short of the flange then caulk the joint well.

Jaz