Is there a way to import customer payments where External IDs are used as reference type for the invoices paid? The documentation says yes. I also have a vague recollection that I was able to do it before. But at the moment, when I click the pencil icon for the invoices, it doesn't give me an option to change the reference type. The same goes for Vendor Bill Payments. I also don't have the option to choose External ID for the bills paid. Seems odd.

is it via CSV import? If so yes it is supported via External ID, I just created a saved csv import for one last week. You will want to make sure the field is mapped first before click the pencil icon to change the reference type.