Efile is only looking at the EIN, not the names. Yes, if you enter each W-2 separately (with same EIN), it will probably result in an efile error for a duplicate W-2.
If the two entities both have the same EIN, they are most likely considered one entity as far as the IRS is concerned, so you can make one entry, combining the amounts.
Click this link for more info on Multiple W-2s.
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