If your Efile is Accepted, don't worry; the Employer ID number is not essential to filing a correct income tax return.
If your return is Rejected, you'll be able to open it and change the number (along with anything else you need to fix) and Efile again.
Click the link for info on how to Check Your Efile Status.
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I have a similar situation. They had multiple fed id's because everyone is under one umbrella with multiple names. I was given the fed id for rex payroll , but w2 shows physicans network again thease companies are one company and recently went through name change at end of 2019 and will start using same fed Id this year 2020. My return was accepted and I'm wondering because it's a unique situation if it matters the fed Id is different