While I don't know how well it works with currently active/open or system files FreeFileSync allows synchronization based on one of 4 options
- Synchronization of two locations (add/edit files on one location and the same will be done on the other)
- Mirror the source onto the destination so the destination is a copy of the source
- Update the contents of the source that is not located in the destination, even if the destination has files the source does not
- Custom
It could be set up for "real time" so at some determined number of seconds (like 10 seconds, the default) after a file is added/edited/deleted, FreeFileSync will scan the two directories and perform whatever you chose to do.
Or you can set it off manually or add it to a Task Schedule.
It is like Dropbox or SkyDrive except you can choose whatever directories you want and it can easily back up to a mounted external drive.
On the destination, the files will be exactly as they are found on the source so grabbing single files is available.