Actually, you can have the same user name on both the directories. And you can also specify which directory has the priority.
I haven't tested this before but I assume if would be fine. You can import the data into a test instance, create a new directory that connects to LDAP, move the LDAP directory above the internal directory and things should be fine. Test it first ;)
That what I did in the past (when migrating users to LDAP/AD) too and it worked for me
Actually I strongly advise for having exactly the same usernames in LDAP as you had in JIRA - you will face the least pain. Otherwise be prepared for manual migration of usernames to match new LDAP ones (aka XML or DB hacking).
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