When an analysis configuration is created a user will follow the wizard, to set a transformation target(s), select packages, etc.

Upon reaching the Review screen, with the button available to Save and run, if the user decides to navigate back to any of the configuration screens and make an update, e.g. change the transformation target(s), then the changes will be lost unless the Next button is pressed.

Workaround
Always use the Next button to advance after applying any change to the analysis configuration settings.