If the payslip is correct, you just need to pay an adjustment to match it through your bank account. The STP should be fine, as it would have been based on the payslip. You wouldn't do an extra payrun, as the correct amunt has already been recorded.
For example, the pay slip says that they should get $100, but they have only received $80 so far, due to less tax being withheld. Pay them the extra $20, which has already been recorded, but is sitting in your bank suspense, or wherever your pays come from. Or, depending on how you process pays, your bank account doesn't reconcile. You don't have to record it again.
It also goes without saying that you should let your employee know so they don't get confused, and adjust it for next pay so it doesn't happen again.
Thanks for your help, I am glad you understood what I was saying. The payslip is correct and there are the 2 separate bank feed transactions to account for the full amount required (just like your example).
I am not sure how to process the 2 separate payments. From looking at other community threads it seems like everyone is recommending to create 2 new payslips with the correct values (reverse the original) or make an adjusting journal after discussing with an accountant.
You could reverse the original payslip, and then do 2 new payslips to reflect the 2 amounts paid on different days (I presume).
If you have an accountant, ask them how they would prefer you to reflect this.
As it stands, the payslip total now matches the bank total, so you should be able to reconcile by adding the 2 payments together(in your head) and ticking them manually if they don't match automatically, unless you had a bank statement issue in between the 2 payments. In that case, you would either need the 2 payslip option, or an adjusting general journal putting the outstanding amount into bank suspense until it hits the bank, and then using another GJ to put it back in the bank. Similarly to how you would also treat a bounced payment due to incorrect bank details.
