Do you have access to the floor underneath the flange? If so, the best thing is to just cut it out, raise it and install it ON TOP of the finished floor. It should be supported by the finished floor and screwed down through it. Now, it can be a pain to drill through the tile, so many people make slots when setting the tile so they don't have to drill later.
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You could stack some flange extenders on and a repair ring, but if you're goin gto all the trouble of making a nice new floor, why risk things by having all of those pieces leaking or coming loose?