No. The only way that could happen is if the mod is from before the detrimental effects window went in, because even with a new mod even if you deleted that file from the folder, it would still fall back on the default version.
Open your eq2ui_mainhud.xml file in a text editor (like notepad -- don't use word or anything formatted). If it doesn't have this line, add it somewhere (just not after the final </Page> at the end)
<include>eq2ui_mainhud_detrimental_effects.xml</include>
That'll add the window for ya and stop that annoying pop-up message.
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