i changed the old serial numbers and the different region to same with my banned 3ds' serial numbers and also the region too on friendseed file while i transfer it to my banned 3ds. how can nintendo see the difference?
If you've miraculously moved your NNID over without system transferring/using support - that's definitely 1 way they can (point about having all transfers on record).
There could be another means, like a backup console ID somewhere we haven't found yet (which they can use to cross reference the change in ID). It's very early to tell as this is a pretty recent exploit/work around.
There's no telling what Nintendo is up to. After all, the Sun-Moon thing came as a surprise (first time it's happened I think), so it's entirely possible they could send out a sneaky update to screw something up etc.