Playing on Minecraft 1.21.1 NeoForge
Using Sophisticated Storage 1.21.1-1.4.41.1186
Using Sophisticated Core 1.21.1-1.3.52.1020
Using Sophisticated Backpacks 1.21.1-3.24.15.1264

Using a number of additional mods, including Create. I am not using a modpack, I have installed mods individually.

I've encountered an unusual behaviour that causes items to disappear. When using Sophisticated Storage shulker boxes (I have reproduced the issue with iron and diamond shulker boxes), I have noticed that when I make use of the feature that allows you to right-click items directly into the shulker box in your inventory without having to place it down first, items that are right-clicked into the box sometimes disappear when saving and quitting the world and then loading back in without first placing down the shulker box. Unfortunately it doesn't seem to happen 100% of the time, but it happens more often than not. I have noticed this behaviour happens very consistently when I right-click items into shulker boxes that are inside of my ender chest. If I right-click items into a shulker box and then place the shulker box down, the items will be safely preserved upon quitting and reloading the world.

Notably, I have not been able to reproduce this behaviour using Sophisticated Backpacks. I have tried the exact same steps with backpacks and have not had any loss of items. This leads me to believe the issue is shulker box specific. I am aware of the issue around compatibility with the mod Quark, but I do not have the Quark mod installed (which to my knowledge is not available for 1.21.1).

Thanks for reporting this. That sounds like shulker data are not marker to be saved when the stashing occurs. I will take a look at that and fix.