do users not in the jira-user group count against license?

We are running a very old version of JIRA that only allows 'deleting' users. There is no option to inactivate users. I'm a little nervous to delete a user so I'm wondering if I remove the JIRA users from all groups, including the jira-users' group will that remove them from counting against our license?

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You're on the right track.  It's not necessarily as simple as "JIRA users".  You need to remove them from any group which lets them log in.  If you check Admin -> global permissions, you will see that lists "Users", "JIRA admins" and "System admins".  Usually, "Users" = "JIRA users", but not always, so it's worth checking.

All three of those permissions grant "can log in and hence take up a licence seat".

This is very helpful and makes complete sense. Thank you very much for your help and quick response.

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