Gary,
The set of targeted catalogs is recorded at the start of the scan. You can safely change those check boxes as the scan continues. You can even change the lists of paths to scan and ignore while the scan continues.
The only thing you can't do is start another one while an existing one is in its first phase (the directory scan phase), but once that completes you can start another. The Scan button will be enabled when it's OK to start a new one.
Changing the targeted catalogs (Add) won't affect the scan(s) that are already in progress.
-Kirk