You'll find the projects share the same workflow scheme, so when you change a workflow in that scheme, it affects all projects using it. You can decouple this - create a new workflow scheme, with its own workflows (copying them is an excellent approach) and set the projects to use different ones.
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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