Major Drawbacks describes what happens when a Major Drawback's mitigated:
Where the GM deems it appropriate, characters may remove a Major Drawback by expending a feat slot gained by level advancement (but not a class granted bonus feat), or through an appropriate quest and/or roleplaying effort over time. A GM can treat the removal of a Major Drawback as being worth 5,000 gp of treasure, and reduce that from the character's share of an adventure's rewards. The same roleplaying that explains how the character overcame the drawback can be tied into the reasons why only that character's rewards are reduced. Of course if all the PCs have and overcome Major Drawbacks, the entire adventure’s rewards can be reduced across the board.
Emphasis mine. That is, what's likely happened is that early in the character's career the character gained, for example, the Major Drawback One Arm or One Leg, and from that gained an additional feat. After some adventuring, the character acquired, for example, a mechanical arm or a necrograft leg that removes the penalty associated with the major drawback and grants the character the benefits of the replacement. The character now has the additional feat for free. This drives the game crazy, so the rules quoted above suggest somehow causing the character to lose 5,000 gp over the course of his remaining career, maybe, for example, by forcing the character to spend that gp on expensive oils, ointments, and salves to avoid his body's rejection of the new arm or leg or by having to pay a healer or similarly equipped veteran for special training that permits the character to master his new arm or leg or by the gods taking their cut of the character's earnings for allowing the character to have an extra feat.
If building a character at higher than level 1 that's already mitigated a major drawback, simply subtracting 5,000 gp from the character's wealth by level seems fair for both you and the GM not having to worry anymore about repaying the character's debt to the universe. The character does, however, risk regaining the major drawback if the prosthesis is removed.