Do unpaid invoices come across in a payment CSV?

Short answer: A payment file imports collected money. Its unpaid invoice balances are not brought into Get Paid.

The review and final receipt name the unpaid invoices left behind and their readable dollar balance. That includes the unpaid remainder of a partially paid invoice. The collected part can still become a payment; the unpaid part creates neither revenue nor a new invoice. Recent imports keeps the same receipt after you close the window. Older receipts may not have recorded this check; re-import the file to record it.

Des distinguishes invoices tracked in DeskOps from unpaid balances left in imported files. A file balance is a snapshot from import time; check the source for what is still owed. Repeated files are separate receipts, so do not add their balances together. Undo removes that import's receipt qualification. QuickBooks' one-time connected import has a separate open-invoice carry path.