After the migration, you have to add the credits (eg overpayment or other credits) back onto the customer record. This article will show you how to add the credits in Lightspeed.
Go to sale (shopping cart) > find the customer and click on their name.
This gives a screen with the ability to add a store credit.
To apply a credit to a Vital invoice: you can not do this at this moment.
However, you can apply the credit to a store purchase.
Rule of thumb: in the system where you created the credit, is the system to pay the invoice from as the systems do not synchronise on credits yet.