Unfortunately, our deposit system cannot read the contents of Shulker boxes. So any content is wiped when they are deposited or offered for sale. Please empty them before depositing or offering them. I will see if I can implement a warning into the system to prevent losses.
[Update] I will not be able to detect filled shulker boxes in the system and warn users not to deposit them. I submitted a bug report to the developer of the affected plugin. Let’s hope that there will be an update.