My employer has given me 2 W2s with the same FEIN. They have deducted excess social security taxes when both W2s are taken into consideration. What to do?

IRS says file form 843, but in the past 3 years it has gone nowhere with IRS. Once they asked me to file 1040-X. Is there a better way to resolve this with IRS? Is there a complaint line? My employer legally has a Common Pay Letter from IRS that entitles them to deduct excess social security taxes and hence will not change their policy.