I don't think it will be a problem for the OP. I've been in several itineraries going from A to C via B on the same ticket where upon check-in I just told the agent to check/tag my bags to B only (where later I would reclaim and re-check them in at B). Simply because either I need something at B out of my luggage and/or simply I did not fully trust the baggage transfer handling of the airline I flew the A to B sector with to do my baggage transfer at B. I've done this several times with different airlines including AC and have never had a problem with the short checking.