Hi. I'm preparing to install tile in my bathroom. First step was to remove 1/2" particleboard that was on top of 5/8" general purpose plywood. Now I'm preparing to install 1/4" plywood rated for cement board and tile, over the existing 5/8 plywood. To do this near the toilet and get the plywood under the pvc closet flange, I either have to make extra cuts and end up with unwanted seams or cut out the flange and then replace it when the floor is complete. Seems like cutting out the flange might be the easiest option and also the one that leaves less seams in the plywood and the cement board. Is this the way to go? And, if so, what's the best way to cut out and replace the flange? I'm a bit apprehensive to cut the waste pipe without knowing what to do in advance. (By the way, it's a first-floor bathroom with easy access to the pipes in the cellar.)

Thanks!

First why are you using plywood rather than cement board? You said 1/4" but I assume you meant 1/2". Personally I prefer Hardy board. I would rather see you cut the cement board than mess with the flange. You can get into trouble some times because of the closeness of fittings with a toilet flange. If you cut the pipe before the closet bend you will have to add a coupling to reconnect. Doubt that you have that much room. That means you have to cut after the bend, then add a coupling and pipe and new closet bend and then flange. For all we know right now that flange may fit directly into the closet bend.

What do you care about the number of seams in the cement board? If you can tell where the joist are just make a seam over a joist or make you seams perpendicular to the joist. Cut a piece of cement board to fit the area of the toilet. Cut a hole large enough to fit around the pie. Make it about 1" larger, then rip the cement board through the center of the hole, perpendicular to the joist and slide each piece under the flange.

Thanks.
I'm using 1/4 exterior-rated plywood over the existing plywood subfloor because what's there isn't exterior-rated and everything I've read, including Hardie's directions, call for the exterior rating. I'll then install Hardiebacker cement board before installing the tile.
I'll make the cuts in both the new plywood and the cement board instead of cutting out the flange rather than risk it.

As far as I know they quit making interior grade plywood about 40 or 50 years ago. It's all exterior grade today. The only difference was the glue used anyway.