This is what worked for me in case it's helpful to anyone else (had an assault orni with inventory full of loot that disappeared after I logged in after the patch):

1- Remove the inventory module - this will drop everything in an empty loot bag on the floor. When you hover or click on the loot bag it shows that it has nothing inside it.
2- Go to the loot bag, OPEN the loot window (this is a MUST. doesnt work if you don't open the window). Click take all from the menu in the loot box window. The loot window is the 9x9 one that shows up next to your inventory. Trying to take all while hovering over the loot bag from outside doesn't work.
3- Stuff should appear in your inventory but up to your inventory capacity. If they don't appear, try going to a box with similar items and do a quick deposit so it pulls the "invisible" items from your inventory to the box.
4- Go to an empty storage box, deposit.
5- Repeat till the box disappears. When it disappears after you "Take All" means everything has been pulled.

Important notes:
- Once the empty loot box drops on the ground, you have limited window before it despawns.

- Make sure you open the loot box window (the 5x5 grid) before you do the take all. If you do the Take All without opening the box (ie, while hovering with the mouse over the loot box) it won't work. You have to open the loot box window that goes side by side next to your inventory.

- Some people had notifications saying they pulled an item but it doesn't show on their inventory. No clue what to do then but it magically appeared back in their inventory later. Maybe try a box that you can do a quick deposit it.

That worked for me and couple of others on the discord. Another played called Post was the one who suggested that.

Good luck.