in 2015, I worked half the year at CompanyA and switched jobs to CompanyB sometime in May.

During the 401K sign-up, an error occurred and my full first paycheck (and sign-on bonus) ended up going towards my 401K which caused my 401K account to go over the yearly limit by about $8200.

Fidelity then issued a check to me (taking out some federal and state taxes) for around $7445.

When I received my W2 from CompanyB, box 12b-D did not account for the money that was removed from the 401k account. It lists $17347, if you add the contributions to CompanyA, then my W2s still look I contributed $26200 to my 401k even though the money was removed from the 401k account.

Since a 1099-R was issued by Fidelity, that counts as income and the amount over the limit is also being taxed.

My tax accountant says she is supposed to enter the values as they are on the W2 and CompanyB said they will not issue a new W2 because they were not involved in the refund of the money.

We decided that we will enter a value different from 12b-d, subtract the money that was refunded to me because it's already on the 1099. She says I'll probably get audited and will have to explain it then.

Is there an alternative to avoid paying taxes twice on the 401k overages? If not, is there a better way to do this to minimize the risk of an audit?