How does this happen?
 

Travelled from BOS-YHZ last night on 8896.

Was with a colleague who absolutely needed to travel that flight as well, but booked last minute. So last minute, in fact, that when he booked (Wednesday), there were no revenue seats avail. As an SE himself, he booked a Y seat through the guaranteed seat in economy benefit.

Bittersweet is how many of you may describe this benefit. You get where you are going, but at great cost.

We go to check in and find out that there is TONS of space avail on the actual flight. On wed, avail really was not there, I was checking KVS. But last evening...what a difference. And I am not talking about a few cancellations. The gate agent showed me: 20 people on this flight. CRJ seats 30 more!

What could happen, in a day, to 30+ reservations? I, of course, jump to conspiracy theories, but is there something else that I am missing?

Have you considered the volcano blowing ash a few thousand miles East of you? Boston normally would have at least some Atlantic connections that never made it. Depending on the time of day and the circumstances you could be missing a two or three planes worth of connections.

You know, that might be it. CO has lots of flights into BOS that could connect to YHZ on AC.

If he would have checked occasionally, he might have been able to cancel the expensive booking, and purchase a cheaper one?

You're not missing anything. It's definitely a conspiracy. :p