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I do not think separate syncing is possible. I am no authority on syncing though so I could very well be wrong there.

I have an idea though: if you would talk to your companies IT admin and ask him to give you access to a folder on your companies web server that you can use as a WebDAV. It only takes him to create one folder and give you permissions to access it. Since your data would stay on the companies server, would that be in compliance with your companies security standards? Or can you also not have data on your mobile devices?