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Don't know if this will work but I would just enter a new form with all your recalculated information. Be sure to complete the portion about the prior gain recognized. If that works then just delete the original form.
Again this is kind of a guess but it might help.
Right now what I have done is refigured the gross profit percentage on worksheet B and after putting in the new numbers in the gross profit calculation on the 6252, I changed the amount received for the year to give me the correct recalculated gain recognized for the year. End result is correct, but one would think that the program would have a way to deal with this.