If you have two or more QuickBooks company files for the same company, you cannot merge these company files together into a single file.
A QuickBooks company file cannot be merged with another QuickBooks company file using a QuickBooks product.
Note: Because these services are provided by other vendors, they are not supported by QuickBooks.
Also: Payroll data cannot be merged with third party services or applications. If needed, you may use two files. One will be used to enter and process all payroll transactions. The second file will be the file that houses all company transactions.
Once you have processed payroll and paid out liabilities from the payroll file, enter an adjusting journal entry into the working file to reflect changes to the liability accounts as needed.
If this information does not answer your question, you can read discussions and post messages and questions relating to your issue on the Intuit QuickBooks Community site for free. You can contact an agent for additional guidance. Fees may apply.