How to prep gypcrete bathroom subfloor that has wood around the toilet?
You've got a sticky wicket of a situation. However, being able to remove the pipe flange was a great benefit. You'll need to build-out the joist under the wall with layers of 2x6 scraps until the scraps protrude at least 3/4" beyond the wall plane for good support of the new subfloor &amp; the ability to screw or nail.

To cut out the old subfloor, lay a bridge of plywood over the wood area, from Gypcrete to Gypcrete. Drill holes in the wood area, inside of the joist, to poke a tape measure down. Then, set your circular saw's blade depth to the measurement from the bridge's top &amp; down to the bottom of the subfloor.

Then, you'll want to remove the nails &amp; cut 3/4" over or on top of the joists (likely a line where the old nails were), so the new subfloor can rest on half of the old joist. Once the wood floor's out, you can use it as a template for a drop-in plywood replacement. You can do cement or cement board on top of the new subfloor patch.