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Not sure if this will fix your problem, but I always make sure to fast travel to my base of a safe house every time before logging out. I have a fear that if I just shut down the game in the middle of no where, when I come back my stuff will be missing.
Apparently still not fixed. Just lost all (6) of my High End backpacks including the one that was equipped with the Mods I favor most. Very distressing! I do not trust this game now, so why play it? I wish I had not paid for the season pass, and will advise all of my friends to avoid this game and the DLC expense until this is provably resolved.
I lose weapons and gear daily. I continue playing and some of the gear comes back later some doesnt. On the start up screen where you pick a character my guy shows 4 weapons equipped and when I load in the weapons showing from the start screen are gone and my guy has no weapons equipped. Definitely frustrating. The DPS glitch is probably my least favorite since it makes it really hard to perfect your build.