updateProject from JIRA Command Line Interface (CLI) lets you set the workflowScheme for a project. You can use one of the runFrom actions to do this across a number of projects.
Hey Beena,
This seems to be a feature request that has yet to be implemented : https://jira.atlassian.com/browse/JRA-9363
My suggestion is to vote on it to increase its popularity and add yourself as a watcher to receive future updates.
Cheers,
Andre
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