The Apex Predator

I killed the hundred foot shadow with the screaming eagle equipped in the off hand of my second weapon slot but it did not upgrade.

The item was not corrupted, the prophecy was active both times (showing on prophecy screen and quest list) and upgraded fine upon killing the hundred foot shadow again with the item in my inventory.

But I imagine the inactive weapon slots not being checked for prophecy items is a bugg; a potentially costly one as well given some items are upgraded via map bosses.

Weapon swap doesn’t count. Either have it in use or in your inventory. That’s how it’s been since they let you have it in your inventory instead of actually in use. Not sure it is unintended.