Malsua: We pulled off the top 3/4 plywood sheets and replaced the works. Was a much better surface afterwards anyway.
I like this idea - just ripping off the upper layer of the subfloor and starting over from scratch.
It sounds like it would make the project much, much easier, both from the point of view of tearing out the old stuff, and from the point of view of installing the new stuff.
Speaking of which, have you thought about what the upper layer of the subfloor is going to look like after you're finished with all of this DRY ICE/BLOW TORCHING/CAUSTIC ACID/HYDRAULIC HAMMERING?
The surface of the moon, maybe? The Gobi Desert? The Bonneville Salt Flats?
Personally, I'd much rather have the new subfloor to work on.