QuickBooks Desktop and QuickBooks Online are built on two separate platforms, clerk12.
Because of this, certain types of data, including payroll transactions, are not automatically transferred over. You can read more details about this here: Learn how features and data transfer from QuickBooks Desktop to QuickBooks Online.
While many standard payroll items are converted, specialized items that are not supported in QBO may not. Can you tell us more details about the department's gross pay items? We just want to make sure we figure out what happened and provide the correct information about this.
In the meantime, follow the steps in these articles on how to manually add pay types in QBO:
Let me also share this article for additional guidance after migration: Learn what to do after you move from QuickBooks Desktop to QuickBooks Online.
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