If the flange is secure, you actually can leave the flange "as is" with the layers right under the flange ring. I write that because if you damage the flange it can create a whole new can of worms if the flange or flange-to-pipe connection was damaged and had to be repaired/replaced.

However, I'd cut the plywood back closer to the flange, I'd cut back at least to the same size as the first layer that's on top of the plywood in the photo.

You might find that the closer to the flange you cut, you can then dig out the layers under the flange. If you get there, then you can simply install new layers of your flooring sandwich around the flange. The new layers don't have to go under the flange, the new layers can encircle the flange. However, if yo have, say, a 3/4" gap between the top of the subfloor and the bottom of the flange, then just cut some small wood blocks (say four blocks, 1" square and 3/4" high for example or sized as needed) that will fit snugly between the flange and the subfloor, and set the blocks around the flange at the 3, 6, 9, and 12 o'clock positions. Keep the blocks clear of the flange bolt locations.

The flange itself should be securely attached to the waste pipe beneath.

Use a putty knife or equivalent to scrape away the residual wax.

Toilets are pretty easy to install, but if this is your first time I do have a recommendation. Use a waxless adapter. Something like the Fernco. Size the waxless adapter to the size of your waste pipe.

The thing is that wax rings are "one and done" things. If you set the wax ring, then set the toilet, but then you have to pull the toilet up again to reset it, technically you would want to scrap away the deformed ring and install a new ring, even though the ring you just installed is only 10 seconds old. Once a wax ring is deformed you can't really count on it to give you a good seal the second time the toilet is set.

With the Fernco, you set it on the base of the toilet. Then you can set the toilet, pull it, reset, pull, reset, etc. It's good forever, so to speak.

You can set a toilet that is fully assembled. Again if you think the weight might be a problem, you can remove the tank from the bowl. then just position and set the bowl. Then reinstall the tank on the bowl. Then shim the base, snug the bolts, and there you go.

And as always, do NOT overtighten any of the bolts that go through the china. Snug them up but don't crank down so hard that you overtighten them. You don't want to crack the china.

If the base wobbles on your new floor, don't try to make it wobble-free by cinching down hard on the flange bolts. Use toilet shims between the tile and the toilet base. Then snug up the flange bolts.

Buy a new set of flange bolts too.

Good luck and happy toileting!

Fernco and flange bolts. Will do. Thank you so much mongo!

I'm off to trim that plywood spacer (and remove the wallpaper I couldn't reach behind the toilet, and refinish the vanity, and lay backer board, and tile the floor and wall, and then try to replace the toilet. Piece of cake...)

If you decide to cut it off then you'd be surprised at the range of repair flanges out there. It really could be as simple as that.

Then what are you doing typing! Quit loafing around and get to work! lol

Cold, I am too worried to cut it off. This is the house I grew up in, and we have never, ever had a plumbing problem in this house with the exception of a broken hot water heater that drained it's tank into a basement floor drain exactly as it was meant to. The plumbing has always been perfect. I'm just going to cut around it for now. I've measured the "hide" of the toilet and it looks like it'll be OK. I'll do a dry fit before I fasten the backer board.

Mongo, yep. It was a busy day. Tomorrow will be another one! I'll let you both know how it goes.

Thanks again.