When you want to remove a guideline or pathway from the App you will have to remove it from both Media and Content separately.
To remove it out of the media folder, go to Media:
Then navigate down to where the document is kept, using the little triangles to open up the lists. Once you have found the document you want to get rid of, click on its name. Then when you are sure you have selected the correct one, click on Actions in the top right corner. Click on Move.
Scroll all the way to the bottom of the list that opens up, until you see Archive for Toolkits (DO NOT REMOVE). Again, use the triangle to navigate down to the section you want to move your document to, click on its name (a green tick should appear), and click on Move.
You have now successfully moved your document out of the active media folder and into the archive.