If you only wish to credit a pay or self-bill invoice only (not sales), then it is best to manually do this, as explained in the following article:
If you have already created a credit sales invoice and now require a credit for the pay invoice as well then you can do so manually.
Firstly you will first have needed to have created a full or partial credit for the relevant sales invoice from the Invoice Display section.
When you select the Credit Invoice option, the following is shown
It is recommended that you select the Credit Pay & Bill option if you need to fully credit a pay invoice as well. However, if the Credit Bill Only option was selected mistakenly, or if you need to partially credit a pay invoice as well as a sales invoice, then the following method will manually credit the Self-Bill/Pay Invoice as well.
Firstly, when the sales invoice has been credited, a new negative amount timesheet will be created. The credit note for the relevant sales invoice will appear in the Undelivered Sales Invoice section, waiting to be sent. The negative timesheet attached to the credit note can be found in Timesheet Display, as shown below
The original timesheet attached to the sales invoice can be seen, as highlighted first. When a Sales Invoice is credited, a new positive timesheet will be created with the status of Awaiting Approval. This is one created in order to allow any corrections to be made.
A negative amount timesheet will be created as well; this one will be attached to the Credit Note. These two timesheets are highlighted above. The timesheets can be selected by clicking the pencil on the left.
In order to manually credit the Self-Bill/Pay invoice, you simply need to add a new cost to the Pay section of the timesheet
Now you can enter the relevant negative information in costing fields that have been created in the Pay field and then select update
The same amounts must now be entered into the positive timesheet that was also created, in the same manner as mentioned previously. The negative amount, which will act as the Pay credit, can now be seen in the pay column
The credit not for the sales invoice will now need to be recreated from the Undelivered Sales Invoice section
Once it has been recreated, the credit note for the sales invoice can be sent. After this the required self-bill/pay invoice credit can be found in the Supplier Payments section under Create Purchase Invoice. From here you can see the negative amount that was entered into the timesheet
The self-bill/pay invoice can then be credited by creating the remittance advice and subsequently sending it from the Undelivered Purchase Invoice section. This will then credit the self-bill/pay invoice, like the example shown below