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Use good styles, links & bookmarks to-from and appendix* (instead of actual footnotes), save-as docx and convert in Calibre to epub2. Amazon KDP uses epub2 uploads.
Indesign is a kludge / fudge for epub or kindle. It's for PDFs and ultimately print.
Also actual footnotes work poorly and there is no assurance of correct rendering on an app or device.
* Make each footnote one paragraph in an Appendix Chapter. Each one is linked to from source text and has a text [Return to <some named text>] to click on to go back as 'Back' doesn't sensibly return from a link on many devices/apps.
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