It depends where you purchased the e-ticket. If via a travel agent then CX will have no trouble with your friend simply checking in at HKG. It might help if she had a copy of the etkt printout, or at least the ticket number.

If you purchased it on the CX website then what you say is correct in principle. You would normally be checked in at YVR all the way through to BKK. I would call CX and explain the situation and ask them to put a note in your friend's record that you will be flying in from YVR (quoting your PNR perhaps) and I guess it will all be alright.