QB Issue Resolution:

New FEIN typically means New Business Entity.

You should have been using two separate company data files.

Technically, everyone was fired from the old company, then hired by the new company.

Each employee is paid from the two companies, sort of a Before and After. The new company means the wage limits for a lot of tax items restart and they got their own notification as to unemployment and worker comp rates, as applicable and unless there is determined to be a Successor Employer condition.

For instance, the Fed UI limit of $7,000 restarted for everyone, under the new employer.

Resolution for Issue 'How do you issue two W-2’s to an employee because you switched EIN’s throughout the year?' available: Yes (Solved).
Source: Intuit Community forum.

How do you issue two W-2’s to an employee because you switched EIN’s throughout the year?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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