We have the same issue. 
Dropdown delete only works for disabled branches, not for repos.
And it's even worse: Jenkins recognizes the new repo name and also renames 
the display name, which looks like duplicated folders if you don't check 
the URL!

The only workaround I see currently is to delete the folder on disk and 
reload config from disk.

As this seems to be a clear bug, I filed it now: 
https://issues.jenkins.io/browse/JENKINS-64894
This is more serious as it sounds, as it is very confusing for the users 
because of the duplicate folder with same display name. 
Mark Waite schrieb am Mittwoch, 17. Februar 2021 um 15:55:26 UTC+1:

> I've used the "Delete" selection from the dropdown menu to remove 
> individual builds (like the disabled PR jobs that are visible on 
> ci.jenkins.io) and pull request jobs.  Maybe that would work for disabled 
> organization folder jobs as well?
>
> On Wed, Feb 17, 2021 at 6:32 AM Amedee Van Gasse <amedee....@gmail.com> 
> wrote:
>
>> I have a Bitbucket project organization folder.
>> Each repository inside the project is a multibranch pipeline.
>>
>> A few weeks ago one of the repositories inside the project was renamed.
>> The old repository name is still shown in Jenkins, as disabled.
>>
>> How do I remove the old repository name?
>> I have already done multiple scans of the organization folder.
>>
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