I had a similar problem when I was putting down 5/8" engineered
flooring in my dining room. I tried using a leveling compound to fill
in a few low spots. However I wound up removing the compound as I felt
that it might break apart in the future and cause another problem,
especially since I glued down my flooring.
I was told by Bruce Flooring that if I wanted to put down a new layer
of plywood, that it had to be 3/4" inch thick or they would not
warranty their product. Since the 3/4" of the new layer plus the 5/8"
of the flooring would have raised the level of the flooring up over 1
1/4", we decided not to put down a new layer of plywood.
What I did was to rent a floor sander with a very agressive sandpaper
and sand down the high spots. It doesn't have to be perfect but you
should get at least a four foot straight-edge and make sure that you
don't have more than about 1/8" gap under the straight-edge as you
sweep it around the floor.

So far it has worked out OK.

Rich Durkee