Using command line or (Java/.NET) API you can compare a batch of multiple PDF files, e.g. the PDF files with the same name in two folders using the following command:
java -jar java/PDFC.jar -p "folder 1" "folder2"
With the -p command line parameter you can create a PDF file containing the comparison result for each pair of PDF files like you can see it in the i-net PDFC GUI.
For more information please refer to the Command Line section in the documentation:
A Plus license is required to use the i-net PDFC on the command line and/or to use it’s API:
During the evaluation period you can use all features using the trial license.