Yes, credit notes can be manually processed, please check out this article, Creating a Credit note, or follow the below steps:

1. To manually process a Credit Note, navigate to [Documents] [Credit Notes].

2. Next, navigate to the [Processing Credit Notes] tab.

3. Search for the Credit Note number, and click on the number.

4. When in the Credit Note, a yellow [Finish] button can be seen in the bottom right of the screen. Click this button to mark the Credit Note as processed.

The credit note has been processed now, great job!