I recently implemented Crowd for JIRA, Confluence, and Fisheye/Crucible. This involved moving three directories (2x LDAP and the internal directory) from each JIRA and Confluence into the same three directories in Crowd. At this point I plan on deleting the old delegated LDAP authentication directories from JIRA and Confluence as the users coming from Crowd just naturally override the old users.
However, the internal directory is a more complicated issue as it cannot be deleted. In JIRA, I can move the Internal directory higher than the Crowd directory and then delete the Internal directory users one by one (I plan on leaving an administrative account in case of emergencies). This is not ideal by any means, but it works to clean up old data.
I cannot do the same in Confluence. I moved the Internal directory higher than the Crowd directory, but I get errors deleting users "because he or she has authored content in one or more spaces". This seems like an artificial error in this case because I was able to remove two whole directories full of users who have authored content and that content was simply mapped to the new user record from Crowd.
What have others done to clean up old data after migrating to Crowd? I really don't want to leave old data sitting around as it only serves to complicate the solution.