Hi There,
I have investigated the issue and I saw it on the home page but not on other pages. I believe you edit your homepage (and other pages w/ missing elements) on that Cornerstone (3.1.6) version, now that we revert back to Cornerstone (1.3.3) those V2 Sections/Elements become unreadable, hence cornerstone tagging it as missing.
While the immediate advice would be updating X and Cornerstone to the latest version (6.2.2 and 3.2.2), I would not recommend that on the live site. Because your X is coming from an updated version 4.6.4, it is understandable that a) few things will be needing an adjustment/fixing after you update, and b) there is no guarantee that those missing elements will be back after you update, there is a big chance that you’ll be going to rebuild those problematic pages in Cornerstone.
I would advise that you keep your live site as is for now, then duplicate your site on a staging server, you can follow the guide here or contact your hosting to assist you on doing this.
Then do the updates on the staging server (duplicate site) first, then adjust the things that need adjustments. Check the Missing Elements if those were back. If not, then there is no other way but you need to rebuild those pages back in Cornerstone, the good thing is you already have the content (in the frontend, take a screenshot of it) it should not take time rebuilding it.
I understand that this is going to be a time consuming and a might be a little bit hard for you, If you’re not comfortable doing this, I advise that you hire a developer, you can find freelance on online services marketplaces.
Cheers!