I was in my Minecraft World and I picked up my shulker box (Netherite and Ancient Debris) and entered the nether. When I emerged the system glitched and kicked me out when I reenter, that shulker box was gone. Other items were in my inventory, just not that. I have a copy of my world, but it was pre-1.17 and I have collected new blocks and did some modifications to my building.
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Yes the first time the game crashed, I have had now two instances where shulker boxes have gone missing from my Ender Chest. The first time, I placed a shulker box in my ender chest, the game crashed and when I returned to the world it was gone. This time I was putting items in two shulker boxes, I finished, put the boxes back in my ender chest and saved and closed. When I reopened the game, the shulker boxes were no longer in my ender chest. I still have the file open from when right after this happened hoping that maybe there is a backup file somewhere with the contents of my ender chest.

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By "the system glitched and kicked me out", do you mean the game crashed?