I've got the help that you need to get this issue sorted out, @Guy W.

To start with, you'll need to turn off the Automatically apply credits option in QuickBooks Online, so your customer's advance payment will not be applied to the current invoices. 

The Automatically apply credits feature is the reason why invoices are showing as paid since any credit on the same customer will be used to any open invoices.

To turn it off:

1. Select the Gear icon.
2. Click Account and Settings. 
3. Tap on Advanced on the left of the screen.
4. Click the Pencil icon in Automation.
5. make sure to disable the Automatically apply credits option. 
6. Click Save and select Done.

Once done, we can now delete the payment that was associated with the invoice. This way, the invoice will be marked as unpaid, and you can apply the appropriate payment.

Here's how:

1. Open your customers invoice and double click it.
2. On the Payment Status section, click the 1 payment link and tap on the Date hyperlink. 
3. Press on More.
4. Choose on Delete. 
5. Click Yes to confirm.

I'm also adding this link that you can use in managing your customer's credits in QuickBooks Online: Handle a customer credit or overpayment in QuickBooks Online.

Should you need additional assistance about this or with QuickBooks, please let me know. I'll be around for you. Take care.