I find myself in a similar spot. Our disk filled up and seems to have corrupted the RHEL 8.3 kickstart trees, so attempting to kickstart with 8.3 errors out about missing packages.

If I try and delete them in the UI, I get "Repository not found". 

If I try and enable in the Satellite UI, foreman stack traces since remnants of the repo still exist:
Body: {"http_request_method": "POST", "exception": null, "error_message": "Relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [aadf6820-7ca5-477e-a99e-bcd2b19b59ad] conflicts with existing relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [4915c9af-4916-4c36-9fbc-b9cc14fd22de]", "_href": "/pulp/api/v2/repositories/", "http_status": 400, "error": {"code": "PLP0000", "data": {}, "description": "Relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [aadf6820-7ca5-477e-a99e-bcd2b19b59ad] conflicts with existing relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [4915c9af-4916-4c36-9fbc-b9cc14fd22de]", "sub_errors": []}, "args": ["Relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [aadf6820-7ca5-477e-a99e-bcd2b19b59ad] conflicts with existing relative URL [Systems_Engineering/Library/content/dist/rhel8/8.3/x86_64/appstream/kickstart] for repository [4915c9af-4916-4c36-9fbc-b9cc14fd22de]"], "traceback": null}

If I try to delete with hammer, I get:
Could not delete the Repository:
  Red Hat repositories cannot be manipulated.

I did the repository-set command from the original comment, and see the same result so I think the issues may be related?
#  hammer repository-set disable --id 7446 --organization-id 1
Could not disable repository:
  Repository not found

I'm experiencing something like this on Satellite 6.8.5 system.
I cannot REMOVE repo-id 129657.
Here's the repo (note the dupe x86_64_:

[root@sat6 ~]# hammer repository list|grep 129657
129657 | Advanced Virtualization for RHEL 8 x86_64 RPMs x86_64                            | Red Hat Enterprise Linux Advanced Vir
tualization                                | yum          | https://cdn.redhat.com/content/dist/layered/rhel8/x86_64/advanced-vir
t/os       


But the actual -real- repo for that is 319096:

[root@sat6 ~]# hammer repository list|grep 'Advanced Virtualization for RHEL 8 x86_64'
319096 | Advanced Virtualization for RHEL 8 x86_64 RPMs                                   | Red Hat Enterprise Linux Advanced Vir
tualization                                | yum          | https://cdn.redhat.com/content/dist/layered/rhel8/x86_64/advanced-vir
t/os       
129657 | Advanced Virtualization for RHEL 8 x86_64 RPMs x86_64                            | Red Hat Enterprise Linux Advanced Vir
tualization                                | yum          | https://cdn.redhat.com/content/dist/layered/rhel8/x86_64/advanced-vir
t/os       

How can I get rid of that 129657 repo, please? It's been killing my Satellite refreshes.

[root@sat6 ~]#  hammer repository delete --id 129657
Could not delete the Repository:
  Red Hat repositories cannot be manipulated.

@vcojot (or anyone else in this BZ having the issue), I'd like to see some more info from your Satellite's DB if possible:

1) Find the ID for the repository that you're trying to disable via hammer, the UI, or the console (in Vincent's case it's 129657)
2) Find the ID for the product that the above repository belongs to
2) Open up the foreman console (`foreman-rake console`)
3) Show me all of the repository's root info with this command: `root = ::Katello::Repository.find(<repo id from above>).root`
  -> I want to check the root's `arch` and `minor`.  These are used for matching what repository to disable, and I'm suspicious that they contain something unexpected which could cause the `Repository not found` error.
4) Show me the result of this command too: `Katello::Repository.where(root: root, environment_id: ::Katello::Product.find(<product id from above>).organization.library.id).first`

@iballou  I already removed the bad RHEL 8 appstream and baseos kickstarts, but just discovered my normal appstream and baseos repos are bad too.  Here is the information you requested:  

2 Bad Repositories:

Red Hat Enterprise Linux 8 for x86_64 - AppStream RPMs x86_64 8
Red Hat Enterprise Linux 8 for x86_64 - BaseOS RPMs x86_64 8


[root@sat6 ~]# hammer repository list |grep "Linux 8"
1486 | Red Hat Enterprise Linux 8 for x86_64 - AppStream Kickstart 8.3                  | Red Hat Enterprise Linux for x86_64            | yum          | https://cdn.redhat.com/content/dist/rhel8/8.3/x86_64/appstream/kickstart        
1019 | Red Hat Enterprise Linux 8 for x86_64 - AppStream RPMs x86_64 8                  | Red Hat Enterprise Linux for x86_64            | yum          | https://cdn.redhat.com/content/dist/rhel8/8/x86_64/appstream/os                 
1487 | Red Hat Enterprise Linux 8 for x86_64 - BaseOS Kickstart 8.3                     | Red Hat Enterprise Linux for x86_64            | yum          | https://cdn.redhat.com/content/dist/rhel8/8.3/x86_64/baseos/kickstart           
1017 | Red Hat Enterprise Linux 8 for x86_64 - BaseOS RPMs x86_64 8                     | Red Hat Enterprise Linux for x86_64            | yum          | https://cdn.redhat.com/content/dist/rhel8/8/x86_64/baseos/os                    
1016 | Red Hat Enterprise Linux 8 for x86_64 - Supplementary RPMs x86_64 8              | Red Hat Enterprise Linux for x86_64            | yum          | https://cdn.redhat.com/content/dist/rhel8/8/x86_64/supplementary/os             
[root@sat6 ~]# 


Bad Repository ID's:  1019 and 1017


[root@sat6 ~]# hammer product list --organization-id 1 --enabled true
----|------------------------------------------------|-------------|----------------------|--------------|------------------
ID  | NAME                                           | DESCRIPTION | ORGANIZATION         | REPOSITORIES | SYNC STATE       
----|------------------------------------------------|-------------|----------------------|--------------|------------------
143 | EPEL 6                                         |             | Default Organization | 1            | Syncing Complete.
144 | EPEL 7                                         |             | Default Organization | 1            | Syncing Complete.
310 | EPEL 8                                         |             | Default Organization | 1            | Syncing Complete.
146 | OVAL Files                                     |             | Default Organization | 1            | Syncing Complete.
145 | PuppetLabs                                     |             | Default Organization | 1            | Syncing Complete.
282 | Red Hat Enterprise Linux for x86_64            |             | Default Organization | 6            | Syncing Complete.
131 | Red Hat Enterprise Linux Server                |             | Default Organization | 12           | Syncing Complete.
39  | Red Hat Software Collections (for RHEL Server) |             | Default Organization | 2            | Syncing Complete.
----|------------------------------------------------|-------------|----------------------|--------------|------------------
[root@sat6 ~]# 


Bad Repositories belong to Product ID 282


[root@sat6 ~]# foreman-rake console
Loading production environment (Rails 6.0.3.4)
irb(main):001:0> root = ::Katello::Repository.find(1019).root
=> #<Katello::RootRepository id: 28, name: "Red Hat Enterprise Linux 8 for x86_64 - AppStream ...", created_at: "2019-05-22 20:08:50", updated_at: "2019-05-22 20:08:50", major: 8, minor: "8", gpg_key_id: nil, content_id: "7441", arch: "x86_64", label: "Red_Hat_Enterprise_Linux_8_for_x86_64_-_AppStream_...", url: "https://cdn.redhat.com/content/dist/rhel8/8/x86_64...", unprotected: false, content_type: "yum", product_id: 282, checksum_type: nil, pulp_scratchpad_checksum_type: nil, docker_upstream_name: nil, mirror_on_sync: true, download_policy: "on_demand", verify_ssl_on_sync: true, upstream_username: nil, upstream_password: nil, ostree_upstream_sync_policy: nil, ostree_upstream_sync_depth: nil, deb_releases: nil, deb_components: nil, deb_architectures: nil, ssl_ca_cert_id: nil, ssl_client_cert_id: nil, ssl_client_key_id: nil, ignorable_content: nil, docker_tags_whitelist: nil, description: nil, ansible_collection_requirements: nil, http_proxy_policy: "global_default_http_proxy", http_proxy_id: nil, download_concurrency: nil, os_versions: nil>
irb(main):002:0> root = ::Katello::Repository.find(1017).root
=> #<Katello::RootRepository id: 26, name: "Red Hat Enterprise Linux 8 for x86_64 - BaseOS RPM...", created_at: "2019-05-22 20:08:37", updated_at: "2019-05-22 20:08:37", major: 8, minor: "8", gpg_key_id: nil, content_id: "7416", arch: "x86_64", label: "Red_Hat_Enterprise_Linux_8_for_x86_64_-_BaseOS_RPM...", url: "https://cdn.redhat.com/content/dist/rhel8/8/x86_64...", unprotected: false, content_type: "yum", product_id: 282, checksum_type: nil, pulp_scratchpad_checksum_type: nil, docker_upstream_name: nil, mirror_on_sync: true, download_policy: "on_demand", verify_ssl_on_sync: true, upstream_username: nil, upstream_password: nil, ostree_upstream_sync_policy: nil, ostree_upstream_sync_depth: nil, deb_releases: nil, deb_components: nil, deb_architectures: nil, ssl_ca_cert_id: nil, ssl_client_cert_id: nil, ssl_client_key_id: nil, ignorable_content: nil, docker_tags_whitelist: nil, description: nil, ansible_collection_requirements: nil, http_proxy_policy: "global_default_http_proxy", http_proxy_id: nil, download_concurrency: nil, os_versions: nil>
irb(main):003:0> Katello::Repository.where(root: root, environment_id: ::Katello::Product.find(282).organization.library.id).first
=> #<Katello::Repository id: 1017, pulp_id: "64c208a8-9bde-4d29-8d14-d3dd7b33b52a", library_instance_id: nil, content_view_version_id: 1, relative_path: "Default_Organization/Library/content/dist/rhel8/8/...", environment_id: 1, saved_checksum_type: nil, distribution_version: nil, distribution_arch: nil, distribution_bootable: nil, distribution_family: nil, distribution_variant: nil, container_repository_name: nil, root_id: 26, remote_href: nil, publication_href: nil, version_href: nil>
irb(main):004:0> quit
[root@sat6 ~]#

@iballou : I am sorry, I ended up clearing the issue on my Satellite because I needed to recover functionality. My satellite no longer has that bogus repo.

Here is how I resolved the issue:

# foreman-rake console        ----> Let it load.
irb(main:001:0> User.current = User.find_by_login('admin')
irb(main:002:0> ForemanTasks.sync_task(::Actions::Katello::Repository::Destroy, Katello::Repository.find(129657))

# foreman-rake katello:delete_orphaned_content RAILS_ENV=production >/dev/null

Thanks Vincent, no worries. I have a DB dump from Jason now that should give me enough to solve the bug.

Created redmine issue https://projects.theforeman.org/issues/32582 from this bug

Moving this bug to POST for triage into Satellite since the upstream issue https://projects.theforeman.org/issues/32582 has been resolved.

Since the problem described in this bug report should be
resolved in a recent advisory, it has been closed with a
resolution of ERRATA.

For information on the advisory (Moderate: Satellite 6.10 Release), and where to find the updated
files, follow the link below.

If the solution does not work for you, open a new bug report.

https://access.redhat.com/errata/RHSA-2021:4702