I have the following doubts:
1) On a Warpath, land 3 has a Mounded Chiefdom and a Piece Pipe. During the Hopewell Era, a Revolt causes the retreat of my Peace Pipe to number 2. What happens with that Mounded Chiefdom if there isn't a Piece Pipe there when the next turn begins?
The Mounded Chiefdom just waits for the player to spend an Action Point to Advance his Piece Pipe (rule 9.1) -- there is no die roll necessary to due to your previous Mounding. Also, nothing Degrades in the Hopewell Era, your "lost" Mounded chiefdom will patiently await you return.
If I want to incorporate a Chiefdom in land 4, do I have to spend one action point to place the Pipe in land 3 and then try to incorporate it with another action?
Yes, the Revolt does cost you that AP to return -- but your foresight in Mounding eliminates the need to roll for Incorporation (of the Chiefdom in land 3, you still have to roll to Incorporate the Chiefdom in land 4). On Warpaths that are vulnerable to Revolt, I like to end my "drives" in a Wilderness or Mound (or at least a weak tribe) -- nothing is more irritating (in the Hopewell Era) than spending all my AP's to incorporate the "Obsidian" Chiefdom in Dickson, only to watch an Ho-Chunk Revolt roll a "1", sending me scurrying back to Cahokia.
2) Because of the Black Tortoise (additional move), an Army advances on a Warpath and it moves on top of a Peace Pipe. Does the Peace Pipe dissapear as a "normal" hostile advance (the Army retreats away) or it moves on top of the Peace Pipe as a revolt?
The extra Black Tortoise Advance is treated exactly like a normal Army Advance -- the Peace Pipe is expended blocking the Move. Quite often, the involvement of the Black Tortoise will result in multiple Advances, the Peace Pipe will only protect you against the first Advance (at least it is easy to "rebuild" the Peace Pipe when dealing with the BT).