The Masonite coverage was sufficient that replacement was not trivial. Since this is an apartment and not my own home, cost was a factor. The first good thing I did was take out those pieces which had water damage as no solution seemed to make good in that case. The board is just brittle and flakey, so it's not a matter of sticking, but of simple falling integrity.
I covered the rest with a fast drying primer, thinned down somewhat.
The replaced sections use AC plywood, because I couldn't source enough Masonite and needed to finish the same weekend and move in. Now I have something to compare to and I can say both sections appear to be holding equally well.
So the answer is to use a primer over the Masonite and the leveling compound.
One note of caution, the underlayment was nailed down and the subfloor are planks, so it seems some nails were loose in the grooves. Also, I screwed down the underlayment which further pulled down the sheets. Over time I'm seeing small 'pimples' in the floor! I should have taken up these nails. Meh. What are you going to do?