Reply To: Footnotes messing up styles

First of all, I virtually never use the Alt/Option-click to remove formatting anymore. I just click the Remove Local Overrides button. Here’s how to do it and keep your italics:
https://creativepro.com/import-word-files-into-indesign-remove-local-formatting-but-keep-italics-and-bold.php

The Power Styles (part of Blatner Tools or the DTP Cloud service) plug-in from DTPtools.com includes a “remove local overrides” feature that lets you specify exactly which formatting you want to remove and which you want to keep.