When the merge file first opens, only the Output layer and its sublayers are displayed by default.

• Switch layers on and off by clicking the eye  icon next to each layer.
  A layer with an eye next to it is displayed; a layer with no eye is hidden. Note that only one main layer (Input <originalfile>.pdf, Input <revisedfile>.pdf, Output, or Discarded) can be displayed at one time, although within the Output layer or the Discarded layer you can display multiple sublayers at once.
  Note: Layers whose names appear in bold contain content. Layers whose names are not bold are empty.
  Note: If you compare two files with the same file name, the Layers tab displays a date and time next to each file as a way to tell the two files apart.