It’s a new bug connected to the migration to localization, I’m floored that such a major bug isn’t fixed after more than a week. This has the potential to do some serious SEO damage as well.
As a temporary fix, use this code, in the before-/body custom code area.
I’d probably put it site-wide so that it’s easy to add now, and then remove later once localization is fixed.
Note that when localization is fixed, your site will work fine even with this fix-code. However if you actually use localization it will be important to remove this so that your language-specific path redirects work as intended.
<!-- TEMPORARY /en/ bug fix
Remove once Webflow fixes localization.
-->
<script>
// Find all /en/... links within collection list items
const links = document.querySelectorAll('.w-dyn-item a[href^="/en/"]');
links.forEach(link => {
// Remove the /en prefix
link.href = link.href.replace('/en', '');
});
</script>
Question, are you using automated sitemap generation?
I wanted to check if this has broken the sitemap as well but I’m not seeing CMS pages listed at all.
That’s better than broken /en/ links though. 
https://www.atmgeeks.com/sitemap.xml
My approach here is probably the best to safeguard your SEO, so Google doesn’t try indexing invalid URLs and de-list all of your CMS pages. However you could back it up with a wildcard redirect like this just in case anything slips through;
/en/project/(.*) → /project/%1
