Adding my issue to this thread. (not that I think it matters at this point)
I can confirm, this missing item issue has impacted not only the guild bank but all of the personal character banks on every toon i had on this server.
I originally was not going to post when i noticed my Guild bank tabs looked like a checker board of missing items, with some tabs nearly completely empty. This was a server i played back in Mists. I knew most likely anything that was in the bank was all old mats from my gathering and professions, and its been so long since i played on the server there would be know way to remember, although i do have some old Bag-non addon files that would have it recorded. Items that remained was gear and some misc. Drops, looted gear and odly some inscription crafted items
Today i logged a toon and noticed that reagents seemed to be missing from my Toons personal bank as well. Their bags were also a checker board of empty slots. After checking each toon (6) on this server, 99% of the reagents i had from gathering and crafting are gone. (Ores, herbs, bars, anything i would have made or used for crafting). I have nearly nothing for reagents/crafted reagents in my Guild Bank, personal Banks or Reagents tabs. It was because of this that prompted me to post as the issue is well beyond the Guild Bank.
My main server, on the alliance side with most of my toons seems to be OK and not impacted at all.
Here are some details
Realm: Emerald Dream, Horde
6 characters
Professions on these 6 charachters were all maxed out, through Pandaria. Total professions are 4 herbalists, 1 leather worker, 1 enchanter, 1 tailor, 1 skinner, 2 miners, 1 inscriptionist, and 1 alchamist.
I consildated the reagents from the Guild bank and all personal banks and have left the following
*36 desicrated herbs
*36 snow lily petals
*2 rain poppy petals
*17 fools cap spores
*6 silkweed steams
*46 frost lotus
I did find some various inscription inks, maybe 7 different types with various amounts
I took a break for nearly two years. I skipped DF entirely because i was not happy with the direction of the game. I since came back about a month ago for TWW
I think im already regretting that decision. Not because of just this issue, but some other things with the game as well
The silence from Blizz on this is issue says it all.