toilet re-mount with cast iron pipes, no flange

I bought an old house and am currently re-finishing the basement. Everybody told me when I took the toilet out, to leave the flang in and after I installed tile, to extend it up with a flange extender. The only problem is, my toilet isn't mounted with a flange. I have cast iron pipes, so when I started chiseling around the base of the flange bolts so that they would move, all I found was a mounted nut in the concrete floor. Now I have two flange bolts that can't come out or be replaced that are too short to use. Any thoughts about how I re-mount my toilet?

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