New computer - will SB manage the hidden folders?

I have two computers, laptop and desktop, that I used SBSE to mirror the documents folder on each one over to the other, keeping those documents in separate folders. ie on the desktop, the laptop folders are in a folder called "Backup of laptop docs". (and it is not located in any User folders on the desktop).

It also keeps versions on the destination.

I just replaced the laptop computer, and I've transferred all the documents over to it.

Now that there is a new path for the Source on the profile on one computer, and the Destination on the profile on the other computer, will SBSE be able to keep track of the previous versions in the hidden folders, or should I just delete them all and let SB start over as far as previous versions go?

Thanks