In standard D365 Finance and Supply Chain, purchase order line charges are expected to flow to the vendor invoice automatically if:
They are added at the PO level before confirmation,
The charge codes are correctly setup (Vendor Based).
If charges don’t connect automatically, it's usually because:
Charges were added after confirmation or posting,
Charges are not setup correctly,
Since you mentioned using a “Connect Charges to PO” screen, that sounds like a customization, ISV solution, or localization feature, as this screen is not part of the standard product.
In standard flow, you wouldn’t need to manually link charges unless the process was disrupted or extended via a third-party tool. Let us know a bit about your process so we can guide through.
Zain
