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.
I was put in this bug, but I haven't slightly different circumstances. 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 wouldn't think chunk borders would be affected, because both times the shulker box was in my inventory and placed inside an ender chest. If I had to make a comparison to the two instances is, I had exited within a few seconds of placing the shulker boxes in my ender chest. One time the game crashed, the other time I saved an exited. Is it safe to leave items in an ender chest? First time I lost all my netherite and ancient debris, this time I lost all my conduits and beacons. It's making the game less fun when I have to gather all those resources again. I'm using Bedrock on PC.