Blocks with entity models are invisible in debug worlds. This affects:

• chests, trapped chests, ender chests
• banners
• signs
• end portals
• end gateways
• shulker boxes
• skulls
• mob spawners (spinning entity inside as well as flame particles)
• enchantment tables (floating book)

Sometimes punching an invisible block (in creative mode) will make it visible again, but not always and there can also be a significant delay. Sometimes punching blocks (both unaffected and affected) that are adjacent or a few blocks away from affected blocks will make one or some of them visible again. Sometimes punching an affected block that is visible will make it invisible again. Flying around the world will sometimes make affected blocks invisible again after they have already been punched. Breaking particles are always rendered regardless.

Console output repeatedly shows the message "Tried to assign a mutable BlockPos to a block entity...". This is probably the cause of the issue.