[Parody]

It depends on how much you're using the Global Categories and Tag Domains; anything in those may change and new ones may be created that have the same names as yours. You said you're using your own Categories but haven't said how much you're using (and/or how much you've customized) the Global Tag Domains.

One way to see, though, is to sync up (assuming you have Cloud Service) then do the conversion. If you don't like the results, restore from backup or redownload from the server.