Form Cubase's point-of-view, VST2- and VST3-variants of the seemingly same plug-in are in fact different items. AFAIK there is no automated way offered by the DAW itself.
As a semi-automatic workaround, however, I recommend MIR 3D's new preset management. You can save an existing setup as a Venue Preset with a few clicks, including the "Roles" for the instruments. The Venue will be there upon loading the Preset. The tedious part is that you have to manually create and assign these Roles again once you've switched to VST3. But it's straight-forward point/click, really
Sidenote: The latest version of MIR 3D (build 491) suffers from a graphics bug that makes it hard to distinguish between saved and not-yet-saved Roles. I suggest to wait for the update that should be available in a few days and that will fix this problem.
HTH,