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After some discussion we've decided to close this as NOTABUG.
This error (Katello::Errors::Pulp3Error: Validation failed: resources missing ) is indicating that there is data missing in pulp, which can be corrected with foreman-rake katello:correct_repositories COMMIT=true
We run this as part of every upgrade, and a user can run it at any time. Running this automatically i think has downsides, such as causing the migration/upgrade to take longer even for users that do not have any dirty data.
A bz has been open to add this to the upgrade guide: https://bugzilla.redhat.com/show_bug.cgi?id=2027293
Let me know if you have any questions!