It might. When I sold travel, I would print out a consolidated itinerary for the client to give to the agent when checking bags. You might want to contact the airline directly and have your PNR (your passenger name record) annotated for the agent at check-in and make sure that you manually process check-in.

Also, you will want to get boarding passes for your connecting flight so you won't have to go through immigration, security etc. to get your connecting flight.