What happend was that a chest full of items basically dissapeared and also I got a set of duplicates of some items.

So. I dont really know the cause of this, but I thought that I would describe it as good as I can including what I did when this happend.

So every day we have a server restart as part of our daily maintainance (this is fully automatic).
A couple of days ago I was logged in while in a combined spider/skeleton spawner gathering some XP. When I do this I bring all the stuff I need to enchant or do something else to and put it in a chest inside the same room. I keep nothing on me while grinding XP, since sometimes when I go afk for some minutes the spiders might glitch out through the fences due to them beeing so many (or something).
To get there I use 2 sets of nether portals (one to get out from my base and one to get in to the room with the spawners.)

Description of the event:
(This might be a bit detailed, but it is due to that I dont know what is causing this exactly, so I thought I should post as much info as I can)

On this day I logged on, picked up a lot of items from my base and went there, put everything in the chest and started renaming items I wanted to do something with, ehchanted items that needed enchanting, combined items using anvils to get better enchants and repairs of items that were broken.
The items in question were a lot of pickaxes, boots, legs and helmets (all diamond). I also combined two books.
I had renamed atleast 6 items during this time.

At some point in the middle of this, there were spiders getting out and I died (nothing on me except some food). At this point I brought a crappy set of gold and iron armor with enchants on them. I went through the portals from my base back in to the spawning room. Killed off the spiders and continued to fix with the items. I put the iron/gold armor in the chest, but at some point I think that I put it on again due to another spider problem. (I dont remember if I put it back in to the chest after that. I dont think so, but the point is that they had been in the chest at some point).
I also used a bane of antropods sword that I usually have laying in that chest, just in case, but that I am sure that I put back in there.

After this I went on renaming, enchanting and so on. I probably touched almost all the items in the chest in some way.

Anyway.. IThen leaving it afk for a while when my girlfriend came home. After a while, she sat down by my computer and pressed the cross up in the right corner of minecraft, not closing it in the right way. (while I saw it, so I am 100% sure about this).

I didnt think to much about the way it was closed, and I didnt log in again that day. The day after, the server had shut down as it usually does during the server restart, but It hadnt restarted automatically again. (The server admin could not find anythng unusual in the logs). So the server admin restarted the server. Noone else had been in between me and the restart and after the admin restarted the server a friend of mine logged in like 2 min before me and went in to the room to kill of spiders and some skeletons. I came in 2 min after him to the room to get my stuff. However it was all gone except for the bane of antropods sword I usually have there and also the set of armor that I had brought there the other day. (He had not taken anything and I am 100% sure of this).

The really odd thing was that the gold/iron crap armor that I had used to fight off the spiders, and after that put there were all there including my bane of antropods sword. I also had the exact copy of the armor on me, but with 10 less durability (on all items). I know that it is the exact same items, because I usually dont wear stuff like that, and I just picked some random stuff with enchants in my base. The enchants were the same on all items (not very likley when its random enchants dropped from mobs) they were also gold/iron on the same pieces. (and ofc the durability were the same -10)

This whole thing makes me think that the player save and world save got out of sync in some way saving at different times or something. I dont know what happend to the items, and why they all were gone.

But this is gamebreaking and set us back around over 200 diamonds and 1 week of enchanting time to get the right enchants back.

So the problem I would like to report is that it is very important that the players and world all gets saved at the same time and that if something like a crash or desync between client and server happens either BOTH the playerfile and the savefile for the server should be affected or NONE.

This is something that every database manager ever has to think about and it should be the same for minecraft.

So. to make things clear here:
While spiders bugging out or servers crashing are anoyances that, while you dont like them, you can deal with it. Data integrety and consistency of data is a totally different thing and there needs to be some meassures to make sure this does not happen.

(It might be that I have understood something wrong here and the problem is naming or whatever else I did, that is why I included the details, but I think that that is doubtful, and that the problem is some kind of desync, due to the fact that I got some duped items out of it)