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?

Form 843 is your only alternative at present.  There are reasons the IRS may make some changes at some point since there are payroll companies such as ADP who do all the W-2s for different companies with the same EIN.  

Continue to follow-up on your 843 forms because you are entitled to the refund. An excess of social security was paid to the IRS which means they must refund it to you.  

The best resource for you may be the Taxpayer Advocate Service (TAS).  They are in place to assist in situations where you are unable to obtain resolution on your own.

1. You can click here to begin: TAS Qualifier Tool. or 
2. Submit a request for assistance - Form 911 Request for TAS Assistance (instructions are included)
3. Locate the local TAS Office for your area

This will get the process started for you.  It's not going to be a fast process because they are handling a large volume at this time. 

If you do not hear from TAS within one week of submitting Form 911, contact the Taxpayer Advocate office where you originally submitted your request. Incomplete information or requests submitted to a Taxpayer Advocate office outside of your geographical location may result in delays.

thanks a lot for pointing out the resources available. I was not aware of that.

I talked to the IRS agent for one hour. He asked me to fill out 1040X along with Sch. 3. I wonder if this will resolve the issue.