trouble with homasote

Assuming now that you have depression in the layout rather than a bubble, I doubt you'll have much success by pushing up from below on the plywood unless you went to some sort of heat/water/steam method. 

I might try to fill the depression with a floor leveling compound and then sanding and smoothing out.

Are you saying your joists are 2x12s - 4’0” on center with a 2x4 in between a sheet 4’0” on center, so it is sagging rather than buckling.  Huh, I don’t think you should have done that haha.  
At this point I would put in more 2x4 bracing, push up on it with the jack you have to take out the sag, then screw it when it is the best you can get.  To fill in the sagging areas left up top. I would suggest using a floor leveler, a product called Jiff Set.  It is made for exactly that, leveling.  It is like a really fine grout/cement.  Mix it up, pour it on, level with a trowel.  That is what I would do anyway.  Good luck!

@BenLMaggi posted:

Usually for layouts they recommend joists (1x4s usually) every 16". That might be overkill unless you are one of the people who believes you need to build it strong enough to walk on. I think 24" centers is okay if you aren't going to walk on it, as long as you are using the plywood you specified. But 48" spacing... wow, that is quite a gap.

I used Mianne benchwork, and a lot of my spacing is on a 24" grid for support.  I used the Baltic Birch multi-ply 1/2" 11 ply.  I walk on it all the time, no problem at all.

I decided to test the strength of the multi-ply during my layout build.  We supported a 9" wide piece of it on 24" centers and I stood on it.  A sagged less than 1/4", and that's a piece in the open only 9" wide!  I actually did a little hopping on it, and it didn't break!  Supported on all four sides with wood beyond it, I'm sure the benchwork would give out before that plywood moved.

I would jack up a 2x4 with the 4 vertical between the 4x4 opening, screw that in at both ends of the 4x4 opening when level and pushed up in that 4x4 area. If that solves your issue, then going 90° off that, jack into place 1 2x4 between the long 2x4 offset from center, get that level and pushed up, screw that into place, then do the same to the other short side with another 2x4 staggered off center the other way so you can screw that piece in place once leveled and pushed up. Now you have 2 ft spacing instead of 4 ft, that should stop your bowing down. If that works good, repeat with the next section until you brace up your entire layout. Good luck!

"I did notice some slight variation in thickness,..."  Welcome to making things smaller and charging more, where every little thing they shave off saves them tons of money in the long run.  Like plywood, it is all either  metric dimension that they round up to the nearest Imperial Measurement or saving a buck by making a 3/4" sheet of plywood 23/32's.  I'm sure that 1/32 of an inch over a years production saves them millions without compromising structural integrity.