Not every player experienced this issue. For those that did, items which were in their bags when they logged off Monday night were not there when they finally got into the game after patch 3.1 was applied Tuesday evening.
Blizzard blue poster Idrandra gives some specific instructions as to what you need to do to ensure the items are returned. More after the break.
According to Idrandra, if you are missing items it is "recommended" for you to clear your backpack before the realms are restarted. That means you should put all your items in your main bag into your bank before you go to bed.
If you cannot clear out your backpack before the restart happens, clear your backpack out when you login next and then relog or leave and reenter any zone.
Idrandra makes a further note that this fix will apply specifically to "your backpack" and not any other bag. To me this means that it will only apply to the personal 16 slot bag that we all start out with and is glued to our characters.
If warranted, we'll have a follow up on this tomorrow. We are also in the processes of collecting a compressive (and fun) list of bugs that have been and not been fixed in the recent patch.
This fix currently only applies to N.A. realms.