The fix to MC-157133 overhauled the way item stacks are handled codewise in a way that prevents some worlds from being updated to newer versions where the fix is implemented. Included is a world download with 4 problem areas to demonstrate the problem.

The world "Overstacking Problem Demo" includes a storage system containing stacked unstackable items in various containers marked with magenta glazed terracotta: https://www.mediafire.com/file/btlf86ncmaq6w6s/Overstacking_Problem_Demo.zip/file

Loading the world in 1.20.4 yields the following results:
All Containers Marked with magenta glazed terracotta contain stacks of empty shulker boxes.

When separated the empty boxes behave like unstackable items.

The empty shulker boxes cannot be made to stack together again.

Loading the world in versions 1.20.5+ yields:

All Containers Marked with magenta glazed terracotta only contain individual empty shulker boxes, effectively deleting 98.5% of the empty boxes stored by simply updating the world and loading it in the new version.