If you right-click on the workspace you should see Image Container as an option. It must be somewhere in the processes too. I think the keyboard short cut is control-alt-I. Once you have the container you load your files into it, define an output directory, filename pattern, etc. Then you drag the instance triangle onto the bottom bar of the process you want to apply (flip in your case) in a similar manner to applying STF to Histogram. The process will then be applied to each file in the container and the result put in the output directory.
