Allow me to join the thread and help provide additional clarification about importing invoices to QuickBooks Online (QBO).
QuickBooks set fields that you can map when importing invoices or transactions. These are the following:
As of now, you won't be able to map or enable those custom fields added, you need to track it or them manually after the importing process.
You may check this article for further details about importing invoices: Import invoices in batches.
If you have any other questions about importing custom invoice in QBO, just add a comment below. I'm always here to help.