For others looking for help on issues like such. If you generated an estimate that you created the invoice from, open the original estimate that is linked to the invoice in question, and you should see each line item what has been invoiced and what is remaining. Modify the original amount column to reflect the invoiced or paid amount to date.
I create all of my invoices from estimates, so everything is linked back to that estimate id. If you only create invoices, it should still apply the same method rather you will adjust the invoice in question by modifying product or service cost to reflect the amount that has been paid to date.
Save and Close or Save and Send, I save and close, then re-open the estimate or invoice and you will see there is a zero balance, this should also keep your books correct. Hope this helps others having similar issues.
