There was no direct migration option as there is no delegated LDAP, it is Microsoft AD. I just created users and their groups in new LDAP directory and disabled old LDAP one and enabled new one. Then I performed sync.
Users and their groups are fine. But when I look at project roles it is completely different.
Also can you please let me know what other associations can be lost.
Right, so you didn't migrate. The problem here is that a user in directory 1 is not the same object as a user in directory 2, even if the accounts are identical. Removing the old directory means the users have gone, so they'd be removed from the roles
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