Hi Christoph,
In the second instance go to
Process>Modules>Install Modules>Search>Install and you will install missing modules.
Scripts>FeatureScript>Add and you will install missing scripts.
For Favorites, go to Process>Favorites in your first instance of PI and "Save Favorites Process Collection", then go to Process>Favorites in your second instance of PI and "Load Favorites Process Collection"
Regards,
Alejandro.