Our entire JIRA is based on a default workflow. When I create a new workflow and Publish Workflows, I see:
Step 1 of 2: The current status of each issue needs to be changed so that it is compatible with the new workflows.
If I publish the new workflow will it have any effect on the default workflow?
No, the default workflow is fixed and won't be affected.
Other workflows won't be affected either if you create more.
However, one minor note is that workflows often share status. So if you are using status X in several workflows and you rename that status, then it will appear with the new name in all the workflows.
By the way, there's two questions here, one implied and one explicit. I've answered the explicit one (workflows are independent of each other, apart from shared status) The implied one better phrased, and also answered over at https://answers.atlassian.com/questions/10389521/answers/10389551?flashId=1107400394
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