Randem Systems Support Board

Yes, run InnoScript as many times as you need to find all outstanding files after changing the search path or running in 'Safe' or 'UnSafe' modes.
 
This will allow for a better finished script if you allow InnoScript to find and put all available files into your script that it can.
 
For those files that must be added manually, you should use the template processing part of InnoScript. This will allow you to re-run as many times as you need without having to manually add the files over again.