I am preparing to install ceramic tile in our master bedroom. While doing that I will be replacing the toilet. Thinking ahead, will be there be an issue with the level of the toilet flange in respect to the toilet and how they mate up? I will be adding 1/2" of cement board plus tile and mortar and I am afraid there will be a gap.
You'll be adding close to 3/4 of an inch, so you'll need to deal with it. They have "make-up" flanges (not sure what they're really called) in the plumbing department that are designed for just this use. You'll also need extra-long toilet bolts for the flange (unless the makeup one has some provision for putting shorter ones in higher up). I just was looking at these at Lowes the other day and they have at least 3 different options.
We just did something similar, only I just added tile over a slab so it was only being raised about 1/4. Still, I needed the longer bolts and an extra-thick wax ring. I personally wouldn't want to use wax to span 3/4" inch like you have though. If you can raise it up 1/2" then you could use the thicker wax to span the rest.
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