Good luck on this. It should be fine. Also - you can check in for both flights yourself online (separately) and the checkin does not have to be linked (per se) in order to tag the bag through. However, the tagging of the bag is very easy.

The one thing I would do is ask in Vancouver nicely (at any AC airport checkin agent - even at the gate) if they have your bag tag number in your DCS record because if it does not associate properly, the bag may not get loaded - even though it has a tag.

Things are pretty automated now but since a tag can really be issued for any flight on almost any airline - sometimes the information does not feed through (and in the dark old days- it never did - so you had to have it entered manually at the transfer desk).