It's hard to help ATM because your question is fairly open and there is no known bug that would do this. Just fyi: in 8.9/10/11 we added various features, but none should have such an effect. So I'm guessing it's something specific to your install.
So the quick fix: I would roll-back a backup to be online quickly. Then try an upgrade again on a copy to see if it still does this.
If you do want to try to corner the issue, my core question is:
Are you content-items still in the admin-section, are are they completely gone?
Because it's a big difference if they are "deleted" or if they just don't show on the module-instances which should show them.