Happy to give advise on how to handle your customer's transactions, @Liz P. 

I have a solution for your sales order and invoice that are in the close period but have not yet been linked in QuickBooks Desktop. 

I'd suggest re-opening the books so you can link your sales order to the invoice. Proceed with the following steps:

1. Go to the Edit menu and select Preferences. 
2. Choose Accounting, then Company Preferences. 
3. Clear the closing date to re-open the books. 

Visit this link for more details: Set or change a closing date and closing date password. 

Once done, delete the invoice and re-create it. This way, you can link it to the sales order. You can follow the steps provided by MadelynC above. For complete instructions, visit this link: Create an invoice for a Sales Order in QuickBooks. 

Don't forget to receive payments and do a special reconciliation to ensure your books are always up to date.

Once everything's done, close the books again to prevent unintentional changes to the transactions from the previous year. Check out the following article for further details: Close your books in QuickBooks Desktop.

Moreover, feel free to browse these articles below to learn more about managing customer payments, sales forms, statements, transactions, refunds, and credits: 

• Sales and customers FAQs
• Accounts Receivable workflows in QuickBooks 

Feel free to check in later if you still have questions about your customer's transactions. I'm only a comment or post away. Take care!