Fortunately, with T-48-hour check-in, this is somewhat less of an issue because at least you're not flying at the time the second check-in opens.

That used to be a problem with AC - they operated a T-24 system, which was 24 hours before the individual flights. Sometimes the system would let you check-in for the first flight, sometimes not at all. Sometimes the airport check-in desks could take control of the second flight and issue you with a boarding pass, occasionally they couldn't.

The hassle factor was enormous, and - if you were on a fare that didn't allow advance seat selection (e.g. Tango) - all the better seats might well disappear whilst you were stuck at 38,000 feet.

Fortunately they seemed to have solved that now, but it is fairly recent, so there is hope that A3 may eventually follow suit - they are certainly the outliers now in that respect, and it's to their advantage as well because the more people than can self check-in, the less staff are needed to help. Don't hold your breath waiting though!