1. I still edit the homepage using Elementor: https://prnt.sc/nUvXHMJ2ARjV
Maybe the page you want to edit will not be built by the Elementor such as the Shop page. This page will be regenerated by Woo so you will be able to edit this page. So pls let me know the page that you cannot edit. I will check for you
2. Because you still enable the Meta box mode. You should turn it off. Go to Edit page: https://prnt.sc/AnsNkhixTzW_ =>> scroll down and turn the meta box mode: https://prnt.sc/gWRmpm77dwJm then all settings in Theme Options will be applied for your site.
3. Because the new version of Elementor has this problem. This issue has not been fully resolved yet. So for now, each time you edit the Footer, you have to Regenerate CSS and Sync Library: https://prnt.sc/M5W0wOhFnZJ9 (Just do it when you edit the footer only. You do not need to regenerate when edit pages)
Pls check then let me know.