You should be opening the .esp file in Developer Studio. Developer Studio will then update .epx and/or the .xml files based on your changes.
We have one .esp file and three .epx files: pipeline.epx,partial_pipeline.epx and configurationgeneratorForge.epx . When we open .esp file we are able to see pipeline.epx and partial_pipeline.epx but not able to see configurationgeneratorForge.epx . I want to see configurationgeneratorForge.epx in DevStudio so that updating of this .epx is easier.
configurationGenerator.epx is a standalone file, it isn't editable via Developer Studio. I think you could make it editable by creating a new project in Developer Studio, then temporarily replacing the pipeline.epx file with configurationGenerator.epx though.