How are you embedding "zalgo text" in your fanfic to allow your epubs to access it? As far as I am aware, zalgo text is generated by munging characters and multiple diacritical marks together and requires a Unicode font that supports all the needed glyphs and is not an actual font that can be downloaded or embedded. Those blank blocks are generally the result of a glyph that is not defined in the font you are using to display the text.
You might want to try installing the code2000 font on your Kobo and selecting it as the document font.
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