Hi Becca, I was dealing with the same "deleted" employee issue. Quickbooks support was finally able to help me today - they had to "sync our account" on their end - there was nothing I could do on my end.
Our issue: we had terminated an employee in quickbooks online then re-hired and changed their status to active. The employee showed "Active" in payroll and paychecks were being funded but were not showing up on the profit and loss statement. I chatted to QBO support: "I'm seeking help on how to restore a deleted employee. The employees profile is "active" in payroll but there are still paycheck sync errors.", they synced the account & after refreshing it was taken care of for us.
Hope this is helpful for you! Good luck.
