I bought 4 handguns during the frenzy.
I asked for all 4 reference numbers from the retailers and got them.
The next day I emailed the Quebec CFO with all 4 reference numbers, my RPAL, and my range membership in a very polite and formal email explaining I was available for any further questions they may have.
All 4 transfers got finalized within ONE hour of them getting that email. This was in June when the freeze was announced and CFOs were getting thousands upon thousands of transfer requests.
I told another buyer to do the same and she got the same result, same day transfer approval. And no, its not mere luck.
So while you may not know what to do with them (up until now I guess)...reference numbers for store purchases are most definitely not useless.