The flange Carl spoke of may or may not be easily
removed. If not, you can merely replace the subfloor
with 2 pieces of wood fitted to each side and running
all the way on to the floor joists. You may need
to put addition wood under the seam where the 2
pieces meet on each side of the flange. The floor
where a toilet sits should be very rigid, I normally
run a 2x6 cross brace from joist to joist under the
sub-floor just next to the waste pipe.