I'm not exactly sure what you mean but I suppose you want to install 2 Jira's on a server.
If you mean to deploy non-production installations for staging or QA, you could use a developer license, which is available to all existing commercial license holders.
Each single production instance of Jira needs its own license.
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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