Is eHelp's copyrighted Javascript in Air help?

Our software application for Linux is distributed with GNU V.2 license which is fully open-source.  However, we recently discovered that the current documentation generated by Robohelp contains some eHelp-copyrighted Javascript.  This is an issue for us since we are trying to make the application available on various Linux distributions, and they do not allow non-GPL stuff in the distribution.
We also have a Windows application for the same product, and are planning to use Air for the online help.
Can we use Air for the Linux online help? If source code in the deliverable would contain the copyrighted Javascript, is there a work-around?
Thank you,

Can you use cookies with locally installed programs, which is what AIR help is? Aren't cookies for website only?
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