I removed old hardwood flooring from my house which has a 3/4-inch plywood subfloor. Some of the old hardwood (mostly around the edges) had been glued to the subfloor which was damaged during the old hardwood removal. The damage consists of portions of the subfloor having 6- to 12-inch-long gouges (the face veneer and in some cases a portion of the core veneer were detached during the old hardwood removal. See three attached pictures for reference. On my pictures I included the new 3/4-inch, 3.25-wide Brazilian Cherry in the direction in which they will be installed (nailed).

I'd appreciate your advice as to whether I should use a wood filler or epoxy to fill the damaged areas or whether I should replace the portions of the subfloor that were damaged. If wood filler or epoxy, I assume it would need to be one that can be nailed through and that expands and contracts much as wood does, correct? If so, please be specific on the recommended filler or epoxy.

The sub-floor strength will not be compromised by losing some veneer.
A latex sub-floor adhesive will fill gaps to 3/8ths inch. The t&g will hold the flooring in line when fastened with staples nails or cleats when following regular nailing schedule for plank. If the flooring gets fastened too low for the next plank to fit together, gently pry it up so the next plank can slide into place.

Thank you for your reply Pete. A popular latex sub-floor product appears to be Liquid Nails Subfloor. Its technical specs indicate that if offers "good" flexibility which is what I think I would want since it should allow for the natural hardwood expansion and contraction in summer and winter respectively.

If you like you can also put some tar paper down to help level out the low areas.
The latex adhesive will stick to the tar paper and hold it to the sub-floor.