Make sure that you have a backup of the original files before you run the patch!.It's perfectly safe to apply a newer version of the patch on top of older versions.
However, the patch includes mods that will mod Append Set I+II files (if installed).
Note: All mods are optional, so you can select to install only e.g.
AA2Play JS-Frontier 1.40a (v12' 141015) by JS-Frontier English Improved R2.1 by Menelol ( how to use).