I have created a single .iss file that works for both a clean install or a repair, or a modify (if you know which item needs to be selected or deselected in the modify).
Before doing this I put code in my setup to write a 'comment' line into the .iss for each dialog, to make it easier for me to analyze the .iss file.
Create the .iss file for a clean install.
Then create the .iss file for a repair or modify.
Then evaluate the two files using a text editor and create a third .iss file using the text editor starting with the clean install .iss and adding in the entries from the 'modify' that are unique.
If in the two files you have the same dialog header with different responses then you cannot use a single .iss file, unless you first go customize one of the dialogs in the setup and give it a unique ID. Once you do that you can create a single .iss file that will work for either a clean install, repair, modify, or even uninstall.
