I have the steps on how we can add the payment options back to your invoices, outofthechaos.

It's possible that the Online delivery option is set to HTML or Plain text. Let's check your settings and update it by following these steps:

1. Click the Gear icon located in the upper right-hand corner, and select Account and Settings under Your Company.
2. On left of the panel, select Sales.
3. Scroll down and click the Online delivery option.
4. From the Additional email options for invoices drop-down menu, choose Online invoice.
5. Click Save and then Done.

I've added a sample screenshot for your reference:

After the steps above, check to see if your QuickBooks Payment is linked in your QuickBooks account. Then, follow these steps to include the payment options in the invoice template:  

1. Click the Gear icon again and then select Custom Form Styles. 
2. Click the Edit link of the invoice template, and then click the Payments tab.
3. Select the online payment, and then click Done. 

Please see sample screenshot below:

This article includes more details on how to customize your invoices, estimates, and sales receipts in QuickBooks Online.

I'm just a few clicks away if you need more help with invoices in QuickBooks Online. Thanks.