prepping subfloor for tiling

I'm trying to replace the ceramic tile in our bathroom. The problem is that there is a gap around the toilet drain pipe. The subfloor is not quite flush w/ the drain pipe, and there is an even larger 4" x 2" gap in the concrete backerboard that the tile rest on (the previous handyman just filled in the gap w/ putty).
My question is: can can i best fill this gap? my concern is that even if i replace a portion of the backerboard, it won't be supported and the tile or the grout between them will crack. The back corner of the toilet rests in this gap, so there will be pressure on it. Right now I have a shim screwed between the floorboards to support the toilet, but i'd like to have something more durable than a shim. Any ideas?
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davidmc,
You need to add some information please.
davidmc wrote:

Is there a toilet flange on the drain pipe? Is it resting on or attached to anything other than the drain pipe? Is it cast iron or plastic?

I'm still not quite clear on your predicament as to where this gap is and if it is part of the gap you mentioned around the drain pipe. However you may need to go below the backerboard and add some plywood or even below the floor and add a piece(s) of 2X for backing as well around the drain pipe and flange, or at other places where there is no subflooring.
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Yes, there's a metal flange around the drain pipe. 3/4s of the flange is resting on the ceramic tile, but the rest is unsupported w/ no tile or subfloor underneath it. To clarify, the gap is around the drainpipe and the flange. It would be difficult to replace sections of the subfloor b/c it consists of 2 layers of wide, long planks that extend into the next room. I was thinking about using epoxy or something to patch the subfloor, and then replacing a section of the cement board.
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davidmc wrote:

So whoever put in the subfloor (what is the subfloor on?) didn't extent it quite far enough (1/4 the width of the flange).
I don't see that as any big deal, just take up the flange and old tile, re-tile as far as you can.
After all, the flange/tile "as is" has been supporting the john and rider, so will putting stuff back in the same way...no need or reason to make a nightmare job trying to get new subfloor/tile up chock-a-block to the drain pipe.
-- dadiOH ____________________________
dadiOH's dandies v3.06... ...a help file of info about MP3s, recording from LP/cassette and tips & tricks on this and that. Get it at http://mysite.verizon.net/xico
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Put some thin set morter under the backerboard before replacing the bad section. the thin set will fill any voids and provide solid support. Fix any rotten wood in the subfloor before mudding it up. Oil based primer can seal minor moisture problems that have not gone to rot. You might be able to just patch with thinset but I doubt it is that easy, would need to see it to say.

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