We're aware many of you are suffering from disappearing items. We believe this is linked to the same inventory issue that is causing [Connectivity] Infinite Loading / Crafting.
To combat this issue and retrieve your items, please:
  • Make sure your inventory is not at or over capacity
  • Strip any unused weapons of mods
  • Place as much as possible in your Stash
  • Get your backpack inventory as low as possible

After having done this, please re-log. This should normally fix the issue and retrieve your missing items.
This issue should be fixed with the April 12th update.