I think there was a rune downstairs/underneath the floor in the overseer's building. But I couldn't figure out a way to get down there. Any ideas? It's near the area where there's a guy making a speech.
It's in a secret room. You can either discover its location yourself, or, if you handle the target via a certain non-lethal method, you can shadow him to it. If you want I can give more detailed instructions.
A Mission Replay is generally starting that mission all over again. You only get one chance to go through each mission.
For example, even thoguh you go through the distillery district in mission 2 and mission 3, they are technically different. Loot is different, so are runes and bone charms.
For the secret room, either play it so you force Campbell to take Curnow to his secret room and you can see how to get in from there. Otherwise if you saw the secret room through the small window and bars, and are using the heart, it's quite easy to guess it's location, especially if you take a certain route in the Overseer's Office area.
From inside the building, find the door that leads to the Kennels (on the first floor). The first door you'll find will lead you down some stairs, to another door that leads you to the kennels proper. While staring at the zone changing door, do a 180. "Use" the bust that you see and explore.
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You can sneak into the little passageway outside the front door of the High Overseer's Office building. At the end is the little opening that is barred up, and you can actually overhear two Overseers talking about trying to find Campbell's journal. That is what hinted to me in my first run that there was a secret room.