According to the text of Bomb(Su):
On a direct hit, an alchemist’s bomb inflicts 1d6 points of fire damage + additional damage equal to the alchemist’s Intelligence modifier.
According to the text of Bore Bomb discovery:
If a bore bomb strikes a wall, gate, siege engine, or similar large, solid, inanimate structure, it ignores half the target's hardness and deals 1 point of damage per saboteur level.
Now let's see what happens if a Bore Bomb strikes a wall.
- It's a bomb, so, according to the text of Bomb(Su) it deals direct hit damage to the wall plus Alchemist's Intelligence modifier.
- It's a bore bomb, so, according to the text of Bore Bomb discovery we have to check if it hit the wall or another solid, inanimate structure. It is true in this case. Now we reduce the hardness by half and deal one point of damage per saboteur level.
- Let's resolve the effects now. The effects are resolved at the very same time. Damage is direct hit bomb damage, plus Int, plus one per sabouteur level minus hardness. Hardness is half of the object's hardness. Splash damage is dealt according to the normal Bomb(Su) rules.
Once again, this is not a replacement effect. Let's see some examples of replacement effects:
If the weapon's critical multiplier is ×3, it deals an extra 2d10 points of damage instead, and if the multiplier is ×4, it deals an extra 3d10 points instead.
Choose one energy type: acid, cold, electricity, or fire. You may replace a spell’s normal damage with that energy type or split the spell’s damage, so that half is of that energy type and half is of its normal type.
Discoveries, however, don't replace but agument things.
Hope that helps.