Migrations strips out all but one entity embed

I've been doing a lot of testing today & most of the time the result has been the same. My last attempt involved not changing the editor from CKEditor from 4 to 5 before running through all of the cron migrations & that seemed to work. So I think a good trouble shooting note to include in the README file would be that the migrations should run before changing the CKEditor version from 4 to 5.

Are you certain that the embed tags were removed from the content? Using something like the diff module can help you confirm this. I have an issue that looks the same as your screenshots but where not all the <drupal-entity> tags were converted to <drupal-media>. So my CKEditor was breaking and content was being hidden on the full content display when the open and close tags did not match.