The usual process during a COD project is that we create a Quote, Job Card and Customer Invoice. The client then pays the deposit for the invoice. The Customer Receipt is allocated to the invoice created above.
Step 1. Find the first invoice and remove the allocation
Open invoice
Menu>Open in Ledger
Set to active
clear allocation
Set to Complete
Step 2. Credit the initial invoice and allocate the Credit note
Open invoice
Actions>Copy to Credit Note
Menu>Open in Ledger
Allocate Credit note to First invoice Number
Set Credit Note to Complete
Step 3. Re-invoice the updated Job Card
Open Job Card
Action>Create Invoice
Menu>Open in Ledger
Allocate Customer receipt to 2nd Invoice
Set Invoice to Complete