Automator Print Plugin: Append Output to Existing PDF File
A very old discussion on https://discussions.apple.com/thread/2240963 had the solution.

Here is a working version of the plugin:

1   Ask for Finder Items
        Type: Files
2   Set Value of Variable
        Variable: original
3   Run Shell Script
        Pass input: as arguments
        Script: echo $2
                echo $1
4   Combine PDF Pages
        Combine documents by: Appending pages
5   Get Value of Variable
        Variable: original
6   Run Shell Script
        Pass input: as arguments
        Script: mv $1 $3
7   Open Finder Items
        Open with: Default Application


Step 3 solves the problem of appending rather than prepending the file by echoing the items in the reverse order. Steps 2, 5 &amp; 6 takes care of creating a new file by renaming (and moving) the new file to the original.

As soon as I have tested it out more, I will post a link to a working version.