Unusual Circumstance Causing Overpayment of Social Security Taxes

I have two W2s coming from a parent company. SS taxes were paid by this company for my direct employment with them. After I transferred to another business unit of the parent company, my SS tax withholdings were reset to withhold as if none were taken previously. This is due to the fact that the business unit is legally a separate company from the parent as far as the IRS is concerned. However, the parent company provides the W2s for the business unit, acting as an agent for that unit. The second W2 for the business unit uses the name <Parent Company> acting as agent for <business unit>, and uses the parent company's EIN. The result is the my SS tax was over-withheld between the two W2s. In the past, this was not an issue when using TurboTax, since it keyed on the name to distinguish the companies. However, now TurboTax keys on the EIN and will not allow proper handling of the over-withheld tax. My refund should be coming through the IRS - not from the parent company. How do I address this in the TurboTax software?