As far as we can see, in the first crash, they were deployed and then raised again. It may have been the 5 second time delay that masked the benifit from the PF.
By this I mean, they were lowered again, and for a few moments things looked hopeful. With limited knowledge of the system interconnection, it seems reasonable to raise the flaps again. When they were raised, MCAS had reset but the subsequent delay allowed the PF's mind to go on to other things.