The bug

Normally you aren’t able to destroy netherite when thrown into lava, however this mechanic can be bypassed by putting netherite into a container such as a shulker box, a chest with an NBT, or a bundle (see MC-204146), then throwing the container into lava.

This is most likely caused by the fact shulker boxes, chests and bundles can be burnt in lava, and when they are burnt, all of it's NBT data gets deleted regardless of whether the item is fireproof or not.

How to reproduce

1. Throw a netherite ingot into the lava
   → The netherite ingot isn't destroyed
2. Put the netherite ingot into a shulker box, a bundle, or summon in a chest with an NBT.
   → All of the contents of the container is destroyed by lava, including netherite, when thrown into it

Someone has made a datapack that fixes this issue for shulker boxes. https://www.planetminecraft.com/data-pack/netherite-items-come-out-of-burnt-shulker-boxes/#
Be mindful that this pack has a bug where sometimes the netherite is invisible when coming out of burnt shulker boxes. Relogging should fix the issue.