Why did you use MS Word?
Open the exported docx on LO Writer. Save at once in odt
Then adjust styles (One style edit will fix footnote size) and fix anything broken.
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So that, I can click on the foot number to GET to the footnote, but not on the corresponding link on the footnote to get back to the text.
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That's easily fixed, if broken at all on a direct import of docx
Or try RTF from Calibre.
But I still don't understand the logic of converting epub (best ebook format) to PDF (really for Print or print replica and not actually an ebook at all).
But if you have an MS Word that exports PDF, you don't need LO Writer. Only import a docx from Word2007 or later if going Word->LO
Office97 to 2003 use doc for Word to LO.
Before Office97, use RTF for Word to LO.
But LO is for people that stopped buying MS Word 15 years ago.
Also Word has styles. One style edit will change size & font of all footnotes.