Thanks for letting us know about this issue. I'm assuming you're running with Standard auth mode? I've tested this myself now and can confirm there is a bug where existing user invitations enter a broken state as a result of the 7.11->7.12 migration. Additionally, if the invited user clicks the link they were sent, the invite will not work if it was sent before the migration to 7.12 (more on that towards the bottom).
To make the invitations visible and working again, you can issue this update to your Elasticsearch cluster:
"source": "ctx._source.frito_pie_organization_id = \"000000000000000000000001\""
Now, if a user was invited pre-7.12 and then clicked the invite link after the migration to 7.12 without the above update, my testing shows that the invite will still not work even after correcting the data with the above update. Please let me know if you have users in this state and we should be able to figure out how to get them working again.
I'm going to file a bug report with the team and I expect this to be resolved without the need for a manual update in an upcoming release.