For anyone interested, here is a response I got from a GM on this issue early this morning after servers came back up from the extended maintenance.
"With the Burning Crusade prepatch, all quest items in players’ mailboxes were deleted. This is intended - any quest items involved will need to be reacquired. In some cases, this may mean you’ll need to re-farm those items, or even abandon and reaccept the quest in order to receive the item again. This can take some time, which is unfortunate, but it will be required - these items will not be restorable through the Item Restoration service or by Game Masters.
This also includes Marks of Honor, since these are turned in as a quest item. Marks specifically are not intended to be stored in the mailbox, and would normally expire after only 24 hours. While the maintenance for the pre-patch was extended significantly, this extension wouldn’t have caused any player to lose out on any Marks they had in their mailbox - because the Marks would have already been deleted as part of the pre-patch, regardless of how long the servers were down. Since this is an intended change, the Mail Restoration service will not restore any Marks, and Game Masters will not restore any Marks by hand."