QB Issue Resolution:

No, there is no way to do this with QuickBooks. If your payroll needs to be reported under two different tax entities, then you need two company files in QB (you should start a brand new one and set it up to track the new company.)

Resolution for Issue 'Split company file?' available: Yes (Solved).
Source: Intuit Community forum.

Split company file?: 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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