I have just installed a new floor in the bathroom. What is the maximum space allowed between flange and bottom of toilet?

I think I know where you're coming from. Your new floor now sets higher then the old one so your toilet doesn't set on the flange any more. Right? It would depend on the space between the flange and the bowl as to how I would go about setting the toilet. 1/2 inch or so I would double seal it, (two wax seals) anything over that and they make a wax seal with a funnel that fits inside of the flange so there is no leakage. You still might have to build up the wax seal with a second one but at least you won't have the hassle of raising the flange. Good luck, Tom