There are certain locations that make a shulker box disappear. Other blocks like chests still act normally in those certain places but shulker boxes become unusable and disappear when broken with all the items inside them. Even using a hopper under it, the items from the shulker box cannot be taken out. these are random single blocks and other blocks inside the chunk are ok.

Example in my world (SEED "6939")

Location: -329 | 64 | 99

Another Example: -322 | 64 | 108