For those interested, I played it saved and migrated everything to standard switches.
I migrated the PVLAN to the master vlan. The downside is that the nodes can see eachothers (because they are in the main vlan), the upside is that everything kept on working
Then I copied c:\users\all users\vmware\Virtual Center\ (*) to the same directory on the new vCenter machine, configured the odbc connections and reinstalled using the existing database. All settings were kept (except the active directory logins ofcourse). After that I moved back to the dvSwitch which was recognised by the ESX hosts. I'm fairly sure that if I wouldn't have moved it would have worked as well because the dvSwitch was still "connected" to the ESX hosts via the correct uplinks
(*) If you don't do this, the installer will create new certificates. The impact is that you will have to manually reconnect the ESX hosts.