For a couple of years now I've had great success with Bill Wilson's https://github.com/billw2/rpi-clone for dupicating SD cards on the pi. Great little utility that automatically resizes to fit the card your duplicating to. When I moved to jessie lite last year it still worked great.
However last night with a slightly different jessie lite version it fell over. By that I mean it duplicates the card in the pi slot OK, no error messages, but the duplicated card won't boot, crashes out with "kennel panic - not syncing: VFS: unable to mount root fs on unknown-block (179,7)". This message is double dutch to an old microcontroller bit banger like me so I'm hoping one of the cognoscenti on this forum can offer some kind words of wisdom? The duplicated cards appear to have identical files on them to the original although a Windows PC shows them as to be nowhere as 'full' as the original