Welcome to the Community space, @TW1221.
It sounds like you're dealing with a reimbursement issue in QuickBooks Online (QBO). I'm here to help you with this.
To address this, you'll need to properly categorize the reimbursement so that it reflects accurately on the 1099 form. Locate the deposit transaction and categorize it as a reimbursement to the client. Then, create a new account or use an existing one to track reimbursements.
Once the deposit is categorized correctly, apply it to the customer's invoice. This will mark the invoice as paid and clear the unapplied funds.
After the reimbursement is properly recorded and applied, you can generate the 1099 form in QBO. The reimbursement amount should now be accurately reflected on the form.
You can also review this link to help you learn what you need to do in QuickBooks Online and QuickBooks Desktop if you need to file both a 1099-MISC and 1099-NEC: Modify your chart of accounts for your 1099-MISC and 1099-NEC filing.
If you encounter any issues handling reimbursement, feel free to reach out for additional support. I'll be around to help always.
