What do you mean "piles of stones covering lovely tongue and groove wood floors". Do you mean loose stones? If you want to replace the wood, I would consider what the wood is before putting it back. We have douglas fir flooring in our house and it does not hold up long. By that I mean after 15 years it looks like crap in the one room that we refinished it. It was my husbands office. It is too soft for a long term floor in my opinion. Though we are hard on flooring surfaces because we are on a farm and track in a lot of dirt that grinds the surfaces.

Do you have a picture?

Enduring, thanks for your response. I wasn't clear what I was saying. The stones and wood were under the concrete and tiles in the bathroom. Here are some photos. I would still tile on top of the wood. I think it's such a shame to trash it, when it is still in good condition, and must have played a role in supporting the bathroom floor.

The top photo shows the wood; the bottom one shows the stones under the concrete,Mitch bits of loose tile. Bit like an archeological dig

Should say "with bits of loose tile"

The wood I see in the first picture looks like subfloor to me. Is the board in the right the tongue and groove? I am not an expert, but I would probably take it out and lay appropriate plywood to get the floor ready for the tile system you will be installing. If Bill V. or Mongo don't post, go to the John Bridge Tile forum and ask what should be done. Your floor needs to fit into a limited deflection range before you tile. That includes the proper joist spacing and length, plywood thicknesses and applications, before any durock or other cement board goes down. The cement board is not for strength, only for a surface to lay the tile. So ask more questions and keep taking pictures for clarification. Take pictures with each step. That is my advise, and get feedback from here or the John Bridge forum.

Thanks for your comments and advice. You gave me language to use with the contractor. turns out that he had reinforced all the joists, which meant that the wood boards no longer fitted. And he then laid down durock to create a level surface. This was a very useful conversation for me.