Are you opening eq2ui.xml with uibuilder, and not something else?
And UI builder I (think) may check that all files <include>'d via the eq2ui.xml root are there and if it doesn't find one may throw an error and stop. At least that sounds like a reason it'd do that. Try deleting the include line for that file in eq2ui_mainhud.xml and deleting that file and see if it still does it.
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