Normally, you would run gwcheck before copying the domain and post office just to verify the health of your system.
If your destination server is Linux (SLES) and the source server is not a Linux system, you need to use the dbcopy/gwcheck "storelowercase" function to ensure the files and database contain only lower case characters.
Once that is done, simply install GroupWise 2014 R2 SP2. When you begin your configuration, you want to select "upgrade". You need to do this even thought this is a new install on this server so that you will be given to option to change existing settings stored in the GroupWise database.
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If the users are to be associated with a new tree you need to change the association from one tree to another. If you don't do this the LDAP GUID will still point to the old tree and the user objects will be unmanageable i.e. you won't be able to change the details of the user such as first name, last name, telephone number, etc as that information is managed through iManager.
Nope... when you run the installer it's upgrading the databases not reconfiguring your LDAP setup. The disassociation tool is if you want to remove the associations and have just GroupWise users with no LDAP association.