After asking Support for help, I was sent the url to this link. So it seems like if you're struggling with this issue, the best Xero can do is emotional support. Not actual solutions.
Anyway, my workaround, which is pretty terrible, but the best I can do, is to churn out a list of all the invoices paid on a certain date, then mass send an 'invoice' email, but thanking them for their payment, and updating them on the total outstanding (which should be $0).
Apparently this has been talked about since 2020 (https://central.xero.com/s/question/0D53m00005kdrYoCAI/bulk-receipt-email-from-account-transaction-list) but still no solution.
After asking Support for help, I was sent the url to this link. So it seems like if you're struggling with this issue, the best Xero can do is emotional support. Not actual solutions.
Anyway, my workaround, which is pretty terrible, but the best I can do, is to churn out a list of all the invoices paid on a certain date, then mass send an 'invoice' email, but thanking them for their payment, and updating them on the total outstanding (which should be $0).