I have a few characters that are effectively parked at certain world bosses, and their job is to do them each day. It’s a little bit sad for them, but I digress.
Now, my warrior does kitten, every day. Because the wurm in Caledon starts ‘right’ after that, and I like to try to get in a prime instance, I’ll always run down to the big chest and hit F with my warrior to loot the blues and greens and then logoff immediately (with the little shaky bonus chest in the lower right hand corner for the rare item still there), and bring my Guardian in to get ready for Wurm. 
The next day, I log my warrior in, sometimes not until right before kitten, and collect the bonus chest (still flashing in the lower right hand corner), run to the fort up the hill to the west (near the way point by the next zone) to both do some buying/selling, sell or salvage my rare, etc, and to make sure I’ve moved far enough away that I don’t get hit with the “you are lazy and don’t get a chest today” bug for not having moved far enough away. Has been working great.
This morning when I logged in – no bonus chest was still there from the day before. The blues and greens were in my bag, and I was standing about where the big chest was, I had completed it, but the bonus chest had disappeared.
Is there a new time limit on how long you have to collect those now? Is it possible the process of getting small patches ‘clears’ those?
I’m going to test it again today (won’t know what happened until tomorrow, will come back and report), but wanted to get this out there now in case anyone does anything similar and there really is a problem.