I don't think you can, for the same reasons you cannot sync files from other filesystems in Ubuntu. It is highly unlikely that C:\ on Windows will suddenly disappear. It's equally unlikely that /home in Ubuntu will disappear. Consider a memory stick that's being synced. You need to rearrange your USB devices, so you disconnect it. You then log onto your system and the Ubuntu One client sees that your files are no longer present. Since it is synced, that means it will be deleted on all your other computers and from the web. That is not what you want, but that would be the only way to handle these things. Well ...
It's probably not impossible to find solutions to these kinds of issues, but synchronization is difficult enough when you know what's going on. When you don't know what's going on, as is the case with secondary filesystems, then it becomes very difficult. I would not expect this to be possible at least over the next versions, but then I'm also not a developer of that technology, so who knows. :)
You can try the following, but do so at your own risk... Have backup.
If you are the sole user of the system and D:\ belongs only to you, then you can try to mount it in your home directory instead of as D:. That might work. But DO NOT do that with an external disk, for the reasons explained above.