Description:

When an non-stackable item has its "count" value changed from its NBT, it does not display that in a container, such like a chest, but they are stacked, they just don't show the value, unless you take the item with the cursor, which is a strange and inconsistent behavior.

Re-production steps:

1. Give yourself a Netherite Sword
2. Place down a Chest
3. Put the Netherite Sword anywhere in the chest.
4. Stand on top of the chest
5. Run: /data modify block ~ ~ ~ Items[0].count set value 5
6. Take the Netherite Sword out by hovering over it with your cursor, then click a number on your keyboard like 1, 2 or 3. This will move the Sword out of the chest, directly in one of your 10 hotbar slots.
7. Once you've done that you can close the chest.
8. Now, while in creative mode click E to your inventory and move the item around using numbers on your keyboard as well. You need to move the 5 stacked swords somewhere else around your quick access inventory slots.
9. After that, open the chest again
10. Observe how the 5 stacked Swords just disappear

You can additionally test it with the Test Game that I attached.

Bug Repro NBT Count Chest.zip

Expected Result:

I expected the items to stay, if it managed to enter my inventory.

Actual Result:

They disappeared from my inventory after opening the chest. The swords seem to be gone.

stacking_nonstackables_but_item_disappears.mp4