Julien,
One thing to remember when using Batch Mechanica is that when you setup a Batch run, the current models and analysis setup in your pro/e session are copied into a new folder (name of analysis or design study) on your computer in your current working dir. The files in this new folder are what are use for the analysis run. This means the results will be in another folder inside this new folder that was created.
This allows you to temporarily suppress features
Just change the analysis or design study name for each run iteration you want to run in batch.
Then in Analyses and Design Studies go Run > Batch > give the batch file a unique name and save.
Make additional changes to you analysis setup and then in Analyses and Design Studies go Run > Batch > give the batch file a unique name and save. Just repeat this for each analysis where you need to suppress fasteners or change model geometry and etc.
Remember if you just want to use different load cases or displacement constraints you can set up individual static analysis and reference them in a design study without needing to use Batch mode.
If you have 2 or more different assemblies you can use batch mode to run them back to back.
Loads sets and Displacement constraint sets as far as I know are the only things that you can turn on/off in the analysis definitions. You are not able to turn off fasteners, rigid-links, etc.
