What's even worse about this is that even if a cert number is attached to a reservation (waitlisted for an upgrade), when they reissue the ticket, whoever does it doesn't look at that cert number. They just grab whichever one from your Wallet they want. I've had this happen, and this led to several very long phone calls to get this fixed (and of course at first I was told that it couldn't be fixed). In this case they grabbed one that was expiring further into the future, rather than one expiring soon.
So I'm not sure it even makes any difference if a particular cert is "tied" to a particular reservation. I still try to do that though. But last week I wanted two RUCs tied to a certain reservation (there were 4 in the account, and 2 were already tied to another reservation waitlist), and the attitude I got about it was off the charts. I had calmly explained that though they would see four RUCs, two were already attached to another reservation (which you can't see just looking at the certs), the agent got annoyed about it, started telling me that isn't how the certs work, etc. I asked if she could tell me how they did work, as I always seem to be confused about it, and she wouldn't.