Question: Are there any OpenSource projects which will run in Linux for editing a PDF document, and specifically editing the Acrobat JavaScript within the PDF document?

Answer: 
I couldn't find a solution that exactly met your requirements. Hopefully, the following will provide some help.

1. **PDFedit** - <http://pdfedit.cz/en/index.html>

> 
> PDFedit is a free open source pdf editor and a library for
>  manipulating PDF documents, released under terms of GNU GPL version 2.
>  It includes PDF manipulating library based on xpdf, GUI, set of
>  command line tools and a pdf editor.
> 
> 
> 

**PS** The PDFedit documentation mentions scripting support but does not explicit mention Acrobat scripts.
2. **Multi-platform PDF Editors** - <http://en.wikipedia.org/wiki/List_of_PDF_software#Editors>
3. **Unix and Linux PDF Editors** - <http://en.wikipedia.org/wiki/List_of_PDF_software#Editors_2>
4. **The Acrobat JavaScript Console (Windows)** - <http://acrobatusers.com/tutorials/javascript_console>

> 
> The Acrobat JavaScript Console window (a.k.a. the Console window) is
>  one of the tools included in the Acrobat JavaScript Debugger. The
>  Console window is by far the most useful tool in Adobe Acrobat for
>  testing and debugging JavaScript code, but it is more than just a
>  utility for testing code. It can also execute code snippets for
>  automating tasks in Acrobat and analyzing documents. In this article,
>  we’ll cover setting up and using this essential tool.
> 
> 
>
If you are really desperate, you can open the .pdf file using a text editor. In all of the text you will find the field's Javascript, which you can edit and then save. It is a pain to do, but you can certainly make minor adjustments to the code in this way.

Be sure to make a copy of the original .pdf file as an archive before trying to edit it, of course.