Your PC knows nothing about the symlink or whatever you have called it. It just sees whatever folder you have pointed the symlink to.

The disadvantage is that the notes suddenly become unavailable to the N900 when you connect to the PC in mass storage mode, so you would probably want to close Conboy before doing that each time.

The alternative is to just type cp -r ~/.conboy ~/MyDocs/ before plugging in the USB. Then you have a copy visible to your PC.