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.

If you have a suggestion as to the formulation of that part of the README, merge requests are welcome. Fundamentally, the WYSIWYG/RTE editor doesn't have much to do with what this module does. However, removing support for the drupal-entity tags from the input filter (and the editor configuration, when one is linked to the input filter) will mean the editor does not recognize the tags anymore, and may filter out the unknown tags; it would be critical not to save the resulting content, because that would wipe out the old tags before the module gets a chance to convert them. Also, it would be good to confirm at a HTML level (e.g. by looking in the database) if the tags were removed, or "just" not converted. You may have found another case of the module failing to recognize a certain flavour of entity embed tags.

Disclaimer: this is just what I can come up with what might have happened theoretically.