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how do you change a toilet with four bolts holding it down to a two bolt.
Without seeing it my first guess is that only two bolts are in the flange like you will mount your new toilet and the other two are just lag bolts going into the floor which you can remove and forget about.
Thry this http://www.lowes.com/lowes/lkn?action=howTo&p=Improve/ReplaceToilet.html&rn=RightNavFiles/rightNavHowTo
go down to "Measuring For A Sure Fit "