Sorry, I don’t understand.
By design, Rapid Photo Downloader has no idea if you have deleted images from your computer that you have previously downloaded. All it knows is when it encounters files that it previously downloaded, because it recorded them in a database. This is the exact code where it determines if a file has been seen before.
To select images you can use the mouse and/or keyboard. If you want to then mark them for download, then place a checkmark in one of the selected files to toggle the mouse. I should clarify that part of the documentation, because I can see that as you quoted it, it could be misleading.