I'm redoing a bathroom floor and have a problem where the closet flange is going to be too high. The original floor was a mortar-bed tile installation, so the bottom of the flange is 1.5" above the plywood subflooring. The new floor will be backerboard/thinset/tile, and I think it will only be about 1" thick. The waste pipe is 3" copper with a welded copper flange.

I don't want to tear up the floor after I do this, any advice on how to correct this problem?

The copper flange is soldered on, not welded. This makes lowering the flange much easier then if were cast iron or plastic. With a torch, heat and usolder the flange. Clean any excess solder off the flange. Now take a Saws-All and cut the pipe off to floor level and resolder the flange. Good luck, Tom