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There's nothing except inconvenience stopping you from switching databases on the fly, so long as you always have Internet connectivity. You do have to be sure to sync before switching every time or you will lose changes! Sync, then configure to sync to a different sync database, wait for the database to download, remember you wanted to do something in the other database, sync, configure to sync the other database, wait for it to download, etc. Easy and fun, right? :-)

Is it an actual requirement to keep the data separate, or just something that appeals to your desire to have things neatly organized? If you just don't want to see your personal actions when working on professional matters, and vice versa, it is possible to organize your projects and perspectives accordingly. The basic technique is to segregate the two into separate folders, then make perspectives that focus on one of the folders. You'll only see the actions from projects contained in the focused folder.