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I'm going to disagree with my friend Dave on this one. I have retiled/rebuilt approx two dozen floors over the last ten years that failed as a direct result of a flange being set too low-either because of built up layers of flooring or because it was set too low from the time of the new installation.
If the upper surface of the flange is set lower than the elevation of the horn (the point of discharge on the underneath side of the toilet), then each flush exerts some water pressure laterally. This eventually erodes the wax ring, resulting in leaks that can rot the subfloor over time. This past summer, I remodeled a bathroom where slow leaks from a low flange rotted a couple square feet of plywood and two floor joists. The only thing holding the toilet up was the mud bed. Even the lath had rusted away.
The solution, if time and motivation are in good supply, is to re-rough the flange to the new elevation of the newly tiled floor.
Search way back on this Forum. There is a thread where an explanation is given for proper elevation of a flange.
If you want to re-rough the flange, let us know what the DWV plumbing is (PVC, ABS, cast iron, etc) and what the access from below is like.
1. Is ABS sold in your area? Here in NoVA ABS is hard to find.
2. Is the pipe 3" in diameter? 4"?
3. How close together are the flange and the 90 that's underneath?
4. How close downstream is the next fitting, and what type of fitting is it?
5. Is the plumbing running perpendicular or parallel to the joists? In or under the joist cavity?
See, I told you Rob was a plumber....but...if you are using 1/4" Hardibacker with 1/4" to 3/8" floor tile I still would get one of those beefy wax rings(with horn) and see what you think. Dont use two rings. If you dont think the seal is going to be sufficient then raise the flange.
There are also PVC flange spacers available that have a small lip on the inside diameter, as well as spaces to apply silicone caulk to seal the new spacer to the existing flange. Another method (that I used because I did not have good access from below) was to buy a special plumber's saw - a circular saw device that attached to a drill. You can saw off the drain line from the inside out from above and glue on a new flange at the correct elevation using a union. My plumbing was schedule 40 PVC, so this was no problem. I just needed a long PVC cement applicator to get to the pipe just below the level of the floor.
I have earned a lot of money following up on this approach. A properly installed toilet flange is placed ON TOP of finished flooring. The time to deal with a flange that is not set to the correct height is before tile/substrate work begin.
It is possible to set a flange to the correct height after the fact, but it is necessary to support the underneath side of the flange (unless it's cast iron), and this requires extra work that really can be avoided by doing things correctly in the first place.
I just did one of these things at Mom and Dad's house (pro bono, of course), because the original flange was set too low, the tile installer added underlayment and tile, the plumber tried to beef up a wax ring that didn't seal, the flange broke because it was unsupported, the toilet leaked, the ceiling below had to be ripped out, it will have to be repainted, and so on...
Total time to cut and fit new pipe and set a new flange, including demo? A couple hours max.
You've got an easy job ahead of you. Since ABS may not be available in your area, get a rubber coupling with a shear band for 3" pipe. There are various brand names for these things-one big name is Fernco. The shear band is metal jacket that fits tightly around the rubber coupling and prevents movement/loosening of the fitting.
Since the next fitting is 3' downstream and the pipe is running parallel and inside the joist cavity, you have plenty of room to work. Pick an arbitrary point downstream on the pipe and cut it with a sawzall. Use a fine tooth blade and get a sqaure cut. Clean the burrs off of the edge of the cut.
Before you make this cut, measure the disatance from the cut line to the outside of the hub on the 90 under the flange. The hub is the female opening on the pipe fitting in which the pipe is glued.
Unscrew the flange from the topside and cut the waste section of pipe as needed to get it out from above and below the floor.
Sincce the other toilet is so close to where you are working either plug your cut end of the pipoe with a thumb screw type test plug (about $3-$4) or make sure no one flushes the other toilet while you are working.
Cut a length of PVC pipe equal to the measurement made earlier plus 1 1/2 inches to fit into the hub of the new 90. Prime and glue one end of the pipe into the 90.
Make a reference mark on the downstream end of the PVC equal to 1/2 the length of the Fernco. This will let you know where to slide the coupling to once you have joined up the new to the old.
Slide the pipe and coupling on the old pipe. You may need a little soap to lubricate the end of the pipe. slide the Fernco down so it is centered on the cut ends of the pipes. Rotate the pipe so the top of the 90 is approx level. Put a torpedo level on top of the 90 and go upstairs and look throught the hole to check the bubble. Adjust until it's level and then tighten the bolts on the Fernco.
Glue a section of pipe into the top hub of the 90 so that the top of the pipe is level with the future finished floor. Or wait to do this until after the floor is finished.
Get a flange that glues on the outside of 3" pipe and install on top of the finished floor. Set it so that the bolt slots are lined up so that the bowl can be bolted in the correct location. Screw the flange down with wood screws of sufficient length to go through the subfloor and sufficient size for the heads to catch on the holes in the flange (probably #14's).
Congratulate yourself on saving a couple hundred dollars!