So I'm trying to edit the phpkaox theme.html file, I go in and replace the current file with my edited one, which is as follows:

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Now the changes are uploaded, file is overwritten, then I go to view my new page and the code is gimped, as is it in the theme.html file, it gets turned into this:

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Take note that the javascript reference I had removed is now back, there are way too many tags, tags, basically it's ignoring everything I just changed and reverting back to its old self with my changes appended at the very bottom - doing all of nothing.

Now why is XOOPS re-coding the theme file?

XOOPS can't rewrite the theme.html file (by default, that file isn't even writable by the system). I think you're looking at another theme, or a cached version of it. Make sure your theme is selectable from the themes list, and that you update the template files (both settings can be found at system admin -> preferences -> general settings).

Herko

right - when you change the theme.html file, you need to turn on the "Update module templates from themes/yourtheme folder" setting in general preferences.

Once the theme.html is to your liking, turn the setting off again.

Ohhh - much appreciated.