Currently, Jira does not allow a user (administrator) to change a project key, while editing a project. A work-around is described here: http://forums.atlassian.com/thread.jspa?threadID=12703 . As it is noted, this is very inconvenient operation. I suggest to support project key alteration within JIRA's user interface. This will eliminate all possible errors, humans can make during manual patching of XML backup and folders.

A project key is very likely to be changed synchronously with the project renaming. It would be strange, if a project (say, software project) changes its name, but the key for it still contains an old prefix.

Workaround

Create a new project, and bulk move all the issues into the new project. This way, they will still be able to be referenced by their old key and their new key.