Go to each application and look at "global permissions". That will tell you what user groups are considered administrators. It's quite likely that your current setup says to use the same group(s) for both applications. Add a new group for separate admins, put the admins in it, and apply it to the application you want to separate off, then, finally, remove the shared group from the global permission.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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