Minecraft 1.12
Forge 14.21.1.2426
Refined Relocation 2 4.1.4
Iron Chests 7.0.31.818

I had some Iron and Gold Chests with the Sorting Upgrade. It all worked fine but then I noticed some items just disappeared when I put them in the chest they belonged to. It specifically happened with chests using the Item Match Filter. After exiting the world and reloading the chests work fine again.

Update: It doesn't matter what Filter it is and it happens when the chunks the Sorting Chests are in unloads.