There is no way to go back other than manually doing it. As a rule I never modify any default item. I use it as a base and create a new one and assign it to projects. you could install JIRA on another machine with an evaluation license and look at how it was setup to help you put the setting back.
I think the reason users do this is because there is no other way to modify the permissions scheme that is automatically assigned to new projects when you create them.
Rather than having to go into every newly created project and manually select another more appropriate permissions scheme, it's only reasonable that users end up modifying the default.
In cloud version when you delete the Default software scheme, JIRA will automatically create a new one, when you create a new project. So this might be a workaround.
I do not know about the behaviour on server version.
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