Hey Damian - I just had the same problem. I was remodeling a bathroom when I found one of the floor joists had rotten under the floor planks, so ended up having to replace some of them. Trouble was, the new planks were about 1/4 inch thinner than the old ones.
I laid the subfloor (used 1/4 ply) over the planks, and then used self-leveling underlayment. After the underlayment dried and I made sure it was completely level, I topped it with durock/hardie-backer and began tiling. So long as you're not filling a huge difference (more than 1/2 or so) you should have no trouble anchoring the durock through the underlayment.
Hope this helps!