The exact same thing happened to me on my site https://www.fuchsia-revolver.org. I had a problem with 403 errors showing up on the dashboard, so I used the following fix in my .htaccess file:
<Files index-extra.php>
SecFilterInheritance Off
</Files>
I now notice that none of my links are working – archives, pages, categories, permalinks, etc. This is extremely frustrating; especially since I never had a problem upgrading WP before and am now encountering all of these errors. A site I host also has the same errors.
What do you mean by switching the permalinks to the default style?