My friends and I have found that as long as you don't have more than 2 people in your party it doesn't happen. It is when you have 3 or more people that the loot and xp starts to go missing at the end of missions. It seems random as why is happens with 3 people at first, but we have also found though that is has to do with the amount of loot dropped on the board and in your inventory. If you have full loot bags, you items will disappear. If you have like a page of loot at the end of the mission with 3 or more people, the bug doesn't happens.  

Also there is a bug atm, that if you have full loot bags and have deleted a bunch of items to free up space for better items during a mission, that after the mission when you have cleared your bags, it will tell you, you still have a full inventory. Then upon going to main menu and coming back in , the game gives you bags of loot from previous missions for free without doing a mission. We verified that it is from previous missions as we are getting duplicate items in the free loot upon reentering the game..

To sum it up, something is going on with the loot/item system and multiplayer specifically. It is causing loot to disappear in larger groups (3+) and giving loot to you for free after you have had a mission with large amount of items dropping in groups of (2+). I think something is going on with the server connections between players and something in the system is producing these strange outcomes. The fact that friends and I have had connection issues in missions recently, such as not being synced up mid mission. Points to this as well.  

Just wanted to add a screenshot for the exact problem we just encountered today.

This was during an intel run. Both of clicked "Quit" and the game froze for a minute or so before this prompt. We got our entire progress during the run rolled back. It claims that I lost connection with the game server but I returned to the main menu and was able to play again.

The full clear void crusade did still end, so we cannot rerun it.

I posted a post about this as well here.

Our group experienced the same issue (we lost all loot and xp) four times, last time Friday the 12th of November.

Our group consists of 4 players. We also had almost full inventories of loot at the end of the mission.

After we pushed "quit" there is a delay until the game fades and when we reappear at the ship all xp and loot is gone.

After the fourth time of this happening we reluctantly decided to give up on the game until there have been an official fix. This was heartbreaking because this is one of the most successful games in our group for awhile.

I was playing together with Bjaerni as the loot and levels were lost. Here is some additional information. 

We were playing only campaign missions. We have not tested the Coop multiplayer at all, this bug occurs when a team of players play the standard campaign together as a group. The problems have occurred during two different days (Sunday 10th of October,  Saturday 9th of October). During both times we managed to play one mission without any issues. The second run was problematic. Only the loot/xp gained in the second mission were lost. We did test logging out to the main menu/out of game after the incidents, but did not receive any items/xp after this. The lost loot has never appeared again later. We play the PC/Steam version of the game.

We did a test yesterday with the following changes:

- played with 3 players

- played non-campaign mission

- did not open inventories during the runs as we thought this could be part of the problem

- after finishing a map we tried to stay together at the end and quit from mission almost the same time (we were worried that the backend session was killed before our stats could be transferred back if we quitted the run too far apart from each other)

- we had one mission where Bjaerni lagged badly and disappeared from the rest of us altogether. We finished the map and xp/loot stayed with us correctly. The network lag in itself does not seem to cause this. Baerni was not hosting the map run.

As a result all our runs were succesful (4 runs) without losing any XP/loot. We will need to test more, but the gut feeling is that opening the inventory during a map run might cause this. There also might be differences how this behaves if player is hosting the session or just joining the co-op session. When we lost the gear we did have our inventories pretty full. It is plausible that going over the inventory maximum amount of slots causes this. We also trashed items from the inventory during at least one of the problem runs.

Hope this helps!

Could you rephrase the question, I am not sure I understand what you are asking. I can tell you this though. 

1. We have full loot bags at the end of every mission if I go full bore with high heat. 

2. We have to clear out the bags at least once during every mission because of the spawns. If we don't and leave items on the ground. Items will stop dropping all together at some point.

3. When it happens and we quit to menu and come back, it replicated an inventory of loot from a previous mission to our inventory. I know because I had 3 copies of a lvl 99 armor, 6 enchant armor, I got from a mission. This is after a mission of course, once back on the bridge.

4. Though a few times is has given us less than a full inventory. So it may also be giving us loot that we have thrown away during a previous mission. Those inventories may just be from missions where I took it easy though and didn't go full bore with high heat.

5. I have had it give me multiple inventories several times in a row even though I didn't go into a mission. AKA I quit to menu and reentered 3 times in a row and got a new inventory every time. On the fourth time it didn't give me an inventory. It is like it is tracking a backlog.... 

6. I don't think I have had it happen when I play solo. Though I will pay more attention and test that out here soon. 

@Drizzit We have to clear our bags of trash loot during ever mission, because of the warp spawn. They spawn like crazy with high heat pyskers and the champions are constantly dropping stuff. So I don't think opening your inventory has anything to do with it. The only difference we noticed, is that having 3 or more people in a group causes the game to lose any progress you have made. Like it isn't updating the main server with the mission details once you finish it and quit out with 3 or more people in the group.