I have almost the same question, but I see you have received no replies to your question.
I used to be able to set the older version of this great program so it would [u]not[/u] scan my External Hard Drive.
Since finally discovering the Version 4.5.1 of the Clean Up! Program, there is apparently no longer an option to have that Drive omitted from the scan. If there [u]is an option to omit one Drive[/u] I'd sure love to know how to access it.
So far, all I've been able to do is watch the scan closely, with my finger poised on the key to [u]stop[/u] the scan when it gets to that Drive.
In your particular question, you said your wife is accidentally deleting some files. My only solution to that would be to name yourself as the only one able to run the Program.
Sorry it took me so long to find your post. Even more sorry that, while a few have viewed your question, I've seen no other replies to it.