Well, the thing about saving your workspace...
What it'll do is save only what you have selected, and all of it's child-objects.
IE, if you had the entire "mainhud" tree selected (at the top level) it'll then save every mainhud file, and only those (at that time).
But if you had only a single window selected, then that's all it saves then. I never bother with it -- if you export previously you're good, no need to save workspace.
As for other files... if you've created it, make sure that the thing knows about it. It has to be <include>'d in one of the files that is loaded by inclusion in eq2ui.xml. Otherwise it neither knows nor cares about it.
One other suggestion I have: always export to a "dev" folder. Also, have a "test" folder that you copy only changed things from the "dev" folder to test. And then keep your actual UI folder different, only copynig things over if you're sure you want it, and even then backup the old file.
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