Minecraft version: 1.20.1
Forge version: 47.4.0 (Also tested on 47.3.0 with Iron Furnaces)
Sophisticated Storage version: 1.3.9.1075
Sophisticated Core version: 1.2.23.902

Other Mods:
Iron furnaces 4.1.6 OR GregTech: Modern 1.6.4

Description:
Hopper upgrades void items in Sophisticated Storage blocks when the block they output into is removed.

Reproduction steps:

1. Create a New World with either of the Other Mods above.
2. Place a Diamond Furnace or LV Electric Furnace depending on the other mod chosen.
3. Place a Sophisticated Storage Spruce Barrel atop that furnace.
4. Put a Hopper Upgrade in the barrel.
5. Load up the barrel with Logs (4 or more stacks)
6. Wait for the furnace to fill with logs.
7. Remove the furnace by breaking it.
8. Observe that the logs slowly void themselves over time, as if they were being transported into a container that no longer exists.

I wasn't able to recreate with vanilla furnace, but then tested with iron furnaces and sure enough that shows the issue and the cause is iron furnaces not invalidating item handler capability (or for that matter any capabilities it seems) properly so the item handler of the furnace is still valid even after the furnace has been removed.
This issue needs to be fixed on Iron Furnaces side. I could potentially do a check when neighbor changes if that neighbor block still has the capability, but given that the furnace state (and for that matter state of any block) changes every single time hopper pushes into it that would require spending more cpu power and potentially causing unnecessary lag on what is a bug in a mod.