You can map layers from one layer to another. However, you will want to map all input layers to a version plan layer.
For example, if a layer was spelled correctly in the first layered input file, but spelled incorrectly in a second input file, you could map the incorrectly spelled layer to the correct one.

Figure 1. PDF Layer Selection dialog box: mapping input layers 

Another reason to map input file layers is if the input file contains multiple layers that contain base content. During refine, you can map all base content layers to the base version layer to simplify the input files.

1. Start a refine process on a layered input file.
2. In the Start Process dialog box, click PDF Layer Selection.
3. In the PDF Layer Selection dialog box, click the layer that you want to map, and in the Map selected layer to box, select the target layer.
   The layer mapping in the PDF Layer Selection dialog box is automatically saved with the job in a mapping file (Layer_Mapping.LPV) for future use in the subsequent refine process of input files that contain a similar layer structure. When you open the PDF Layer Selection dialog box, the mapping is already there.
   To use this layer mapping without opening the PDF Layer Selection dialog box, in the Refine process template, in the Normalize section, under PDF Layer Mapping, select the Map PDF layers automatically (by mapping file) check box. This check box enables the mapping file to be applied automatically.
   
   Note: When you rerefine input files or refined files, remapping input layers does not remove any unwanted layers from the version plan. You must remove any layers from a version plan manually. In addition, any colors that were mapped or converted to process during a rerefine may still appear in the Colors to Extract column of the version plan. If you need to make any changes, they must be done manually.

If the mapping was saved previously, and you select the Map PDF layers automatically (by mapping file) check box (Refine process template > Normalize section > PDF Layer Mapping), you can perform the refine process without opening the PDF Layer Selection dialog box (performing steps 2 and 3) as the layer mapping is done automatically according to the mapping in the mapping file.
You can also copy the mapping file (Layer_Mapping.LPV) to other jobs to enable automatic mapping accordingly.
Note: The mapping file is exported and copied with jobs, and is applied from a Template Job.