A refund received from your vendor can be recorded in the form of vendor credits.
A bill that has been completely paid, however, means all dues towards that vendor have been settled, and a refund cannot be subtracted from it unless the bill payment is reverted.
To do this,
Go to the Purchases tab on the home page of Zoho Books and open the Bills section.
Open the corresponding bill under Paid Bills.
Scroll down to the bottom where you can find the payment recorded and hover over it to find the trash can icon.
Click on the trash can icon to delete the payment. The status of the bill no longer shows Paid.
Now click on More -> Create Vendor Credits as shown in the image below. Enter the refund amount and save it. The bill amount is reduced accordingly.