I had an interesting experience last summer where I was flying HEL-GOT on sunday and GOT-HEL-KIX on monday. I had checked in through both flights on sunday, and when I was checking a bag for the HEL-GOT flight the agent automatically checked it for HEL-KIX instead. When I asked her to correct this (I needed the bag for GOT) she said that the system had automatically recognized the HEL-KIX segment when she scanned my passport, as the passport information is not recorded for the Schengen flight (?). I don't know if anyone could use this to their advantage, though.