Manage Labels from Archived Projects
When you use Advanced Label Manager to manage labels in Jira, you might notice some labels without any issues (aka empty labels). If a label is not used in at least one issue, it should not exist.
So, what are these empty labels?
These labels without any issues are from archived projects. When you archive a project, Jira archives all issues and related entities like components, attachments and versions. However, it does not archive labels. Since the associated issues are archived but not the labels, the app cannot find actual labels usage data.
Here is an example:

Labels from archived projects
How to manage labels from archived projects?
If you need to manage these labels (e.g. want to delete them), you can unarchive the related projects temporarily.
Restore the archived projects:
Go to Jira Settings → Projects
Select Archive tab on the left sidebar
Click on Action (…) and Restore

Restore an archived project
Once the archived projects are restored, the labels will show count as usual. All the label management features like editing, merging and deleting will also work as expected.
Show or hide archived labels
If you want to filter out archived labels, you can use the configuration toggle on the left sidebar.

Toggle labels from archived projects
Setting this toggle on will hide empty labels from app dashboard, so you can focus on only active labels.