Maybe I’m misunderstanding your question, but in the footnote options you can set the footnote number to start again on every new page.

Nicole is right. That’s not more action than my suggestion, but you can do more with it.

What settings do you have in the pages panel for that document?

You can try another version of Garamond from Adobe’s Typekit. Or you could change the text to paths.

I found this article in the web: High ASCII Characters Are Not Printed in a QR Code Barcode
(https://help.loftware.com/display/LPSKB/High+ASCII+Characters+Are+Not+Printed+in+a+QR+Code+Barcode)
But I don’t know if this can help. Maybe InDesign treats the special characters in a different way.

Another idea: You could convert the numbering into text: https://creativepro.com/convert-numbering-to-text-in-indesign.php

You can do that with GREP within a paragraph style. Make a new character style and choose the stylistic set you want to apply. Then you can nest this character style into your paragraph style. If you want the alternate character only for the e, just type an e into the field. And you can do this for every character you want.