Is your current bulk sync by user name or email? as long whichever is your key field matches I would think that would make it work. You would have to disable your current sync, then create you new sync set it with ensure the key field is the same turn on your new sync and test.
However as you are a multiple major releases behind and you ware doing this major change you may want to set up a test server with 12.0.1 and clone down the DB make the change and test sync then upgrade or upgrade then make the change. I don't know if it matters which order you would do it in.
Also 12.5.2 is out with multiple additional security enhancements and fixes a major bug with surveys if you use that plus has some additional security enhancements.
Overall installation was seamless. After the new WHD installation, I pointed it to the existing DB (MS SQL 2012 sp1) and it was working well. Since the helpdesk nested in a new windows server, I had to edit the DNS entry. The user LDAP migration from Novel eDirectory to Active Directory on 2012 server was easy but had some user login issue. Users couldn't use their name but were able to use their full email address as their username. No problem to bring up the existing tickets.