When delayItemStackCapabilityInit option is enabled, every item with stack size bigger than 127 which was increased by Stackup! mod, gets deleted in any inventory. If stack size is bigger than 9984, the item count left as minus 9984 of it. (could be depend on max stack size value, I'm not sure)
Joining world specifically affect any container placed in world and opening usual backpack item from mods (or other similar actions) affect whole backpack item slots as well as player inventory.

Disabling delayItemStackCapabilityInit function resolves the issue. Maybe similar case as #79 ?

Tested Loliasm version: 4.11, 4.11.1, 4.12

Logs generated with only Loliasm and Stackup! :
debug.log
latest.log
My config file for Stackup! if you need:
config.zip

Sounds like a coremodding conflict, StackUp patches writeToNBT to change:

nbt.setByte("Count", (byte) this.stackSize);

to

nbt.setInteger("Count", this.stackSize);

While we override the whole method, should be an easy fix.