Save As DocX. Create an epub in Calibre. Check it, upload the epub to Amazon KDP.
Open Office and the better later LibreOffice Write allow you to add notes and link them. Only edit as ODT, with styles. Do an extra Save As in docx.
I can suggest a workflow that's reliable if you like. Don't actually use footnotes/endnotes because if you delete the source reference the note is deleted. Also don't use a small superscript as in paper references. Been working here for years.
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