I'm replacing the sub-flooring and will be tiling. I know that the toilet flange will be low, and it is chipped on one side where the toilet bolts go. I see two options (there could be more...):
leave it alone and once the tile is complete, get a repair plate and build up to correct height.
since there is a stainless sleeve easy to access, replace the complete section and set to correct height before buttoning up the floor