Nic's answer is correct, but having just been through this I wanted to add some detail and an alternative to hopefully save people some time.
In our case, we had "To Do" and "Backlog" statuses in use and wanted to merge them, replacing "Backlog" with "To Do". As Nic says, you can add the new status to the existing workflow and then transition all issues to the new status and switch all your transitions over to the new status. However, you can have a couple of problems:
If you have fewer than 1000 issues and don't care about leaving an isolated, unused status in your workflow then what I'm about to say doesn't matter. However, an alternative to the above is to copy your existing workflow, delete the old status and replace it with the new one, and then swap the old workflow for the new one in each workflow scheme that it's used in. As part of this swap in the workflow scheme, you are asked to map old statuses to new ones, and JIRA takes care of this automatically. I think the only cost of this way of doing it is that you cannot rename workflows and hence you won't be able to keep your workflow name, I just added a "2.0" to the end of my workflow. If you really wanted to keep the name you could copy the workflow, reassign workflow schemes to it, delete the old workflow, then make a second copy and use the original name, make any changes, and then swap back over to this workflow, but I was too lazy to do this :).
Hope that helps! And please let me know if I've missed something in going for this approach.
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