Most entities are invisible after passing through a nether portal placed in the spawn chunks. But only if the entities themselves have passed through the portal.
Approaching from a different portal properly renders previously invisible entities.
This includes at least: item drops, mobs and mine carts.
It does not include chests and other such entities.
I have not found a way to reproduce it but this particular portal is connected to an iron farm.
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I say it doesn't affect Chests, but they obviously cant be sent through a portal like a mob or item can.