I need to delete the 184.108.40.206 version of this add-on so that I can install the free version. What I need to know is if I delete it will it break the dozens of workflows that are using, well rather trying to use it?
Deleting it will break the workflows, but only as they get used. The workflows contain things like "when an issue transitions, do <something>", so if the <something> is "run a script" and the scriptrunner isn't there, it's going to fail.
But if you put back the script runner, that will fix it.
The only issue you might have with the process you suggest is if you have written scripts that only work for 4.1, as the older version won't understand them.
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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