So I am remodeling (because it needs it) a rather small bathroom in my house. I took off the horrible vinyl tiles that were hardly adhered to the crazy thick ~1" particle board that was underneath it. The board also had the added disadvantage of raising the level of the floor in the bathroom to something absurdly over the adjacent hallway. I took the particle board up too because it was also discolored/moldy. The floor underneath that appears to be plywood and was also a bit moldy. I sprayed it down with this stuff that retards mold and mildew growth and says it will help get rid of it when already present.
Are you sure the subfloor is not too far gone? What did you spray on it? If it is in good shape, you need another layer of underlayment grade plywood. Install minimum 3/8", thicker is recommended, then install your cement board into fresh thinset and fasten, tape etc. You wanna install vinyl again? You should be thinking ceramic not vinyl.
TILE GUY - retired- TROY, MI - Method & Product suitability consulting.