Can you not change your passport information on the return?
My last interesting (in this respect) flight was last August, PRG-YYZ-SFO (with an overnight in YYZ). I gave them my Canadian passport in PRG, and then had an agent swap it to my US passport in YYZ.
Obviously a US passport will let you in Canada with no issues for a 16 hour stay, but I still prefer to have the passport on the PNR match the passport (or NEXUS card) I'm scanning at the kiosk.
Or is it just that OLCI won't let you change it, so you have to check in at the airport?