Fortnox has a warehouse/delivery status on orders — a flag that says "this order has been picked and is ready to ship / has left the warehouse." Some Fortnox setups (especially with a WMS or warehouse module) require an order to be in Warehouse Ready / Delivered status before it can be converted to an invoice at all — Fortnox won't allow the conversion otherwise.
So the sequence of events with this setting becomes:
Order arrives from eCom
Junipeer first sets the Fortnox order status to Warehouse Ready / Delivered
Then immediately converts it to an invoice
It's a prerequisite step Junipeer performs automatically so the conversion doesn't fail. If you don't use a warehouse module, this flag is irrelevant and leaving it unchecked is fine.