We are upgrading the bathroom and the floor (ceramic tile over installed over plywood) is out of level and the low spot is around the toilet. I had thought of using floor leveler but I now don't think that will work. It seems like floor leveler would just run down the opening for the toilet drain pipe. Open to any suggestions.
Depending on how large of an area is sunken, you could cut up the old plywood with a circular saw. Sister boards to the joists and add cross members to the cavities to raise the area to match the surrounding floor. Follow up with plywood and then cement board before tiling and you should have a solid, fairly level floor to work with. This can all be done easily even though the basement is already finished. This seems preferential to any floor leveler, since you'd actually be addressing the problem, which is a sunken floor.
It would also be a good time to inspect the existing floor joists and see how damaged they may be. If the damage isn't extensive, doubling them up my suffice, or you may need to replace larger sections entirely.
Self leveling products should normally be no thicker than 1/4 inch.
If it is less than 1/4" difference.
Simply cover the flange hole with anything from a plastic bowl or whatever generic item you come up with.
Rub some oil (cooking oil works) around the edge of the "bowl covering the hole" so when the self leveling product dries, you will have no problem removing the "bowl".