I've noticed the asterisks on all my mod EditorIDs, but I noticed a few EditorIDs in the WarehouseAmbushes. What exactly are these, and how can revert the EditorIDs in the warehouse back to the way they were?

The asterisks mean they are changes belonging to your mod. They appear next to everything that your mod has created or edited, and allow for you to note what your mod is changing more easily.

No way to revert the original .esm files in the .esp back to their original other than reloading the master.esm?

The warehouses don't matter. Nobody sees them in game and it won't affect anything. If you really want to fix it, google "cleaning a dirty edit".

The thing that is confusing me is that the CK says that I've edited cells that I know I have not touched. I did notice yesterday that when i duplicated a vanilla cell, it automatically flagged the original as edited even though i did not even load it up! I don't find this fair as its a practice that has been promoted in the tutorials as a good way to make your own new cells. This didnt happen in past incarnations of the construction set/geck, or am i remembering wrong?

This is not good for my OCD!

- Hypno

^That's a bug.

BUT beware when "surveying" cells with the mouse wheel. You could accidentally move something and it'll flag it.

Better to just set up the ini where you can use more than one instance of the CK. One for modifying and one for searching around vanilla cells.