I have a vendor invoice from 2018 that was paid by a shareholder in 2019. Now I am paying back the shareholder. What is the process to reduce the vendor acct in 2019?

To start with you should for proper digital paper trail have a Shareholder Loan account as a current liability. You may also need a Clearing bank type account but here is what happens.

• you Pay Bills to pay the vendor and the source account is your newly created Clearing bank account (you cannot directly pay bills from liabilities)
• make a Deposit to the Clearing account for the amount paid and post it as sourced from the Shareholder Loan - this zeroes out the clearing account and posts the money owed to the shareholder
• write a cheque to the shareholder posting against the open loan liability

That's not a bad idea. Thank you.

What I thought I might do is: create a credit note in 2019 in the vendor account equal to the amount the shareholder paid and code it to the short term shareholder loan account i created in the GL. 

Then, create a debit note (or add to an existing expense report) the same amount and code it to the shareholder loan account again to offset it. Make the payment to the shareholder for the full amount (loan plus expenses).  

I've already cut the payment to the shareholder that included the loan plus current expenses.