Say a file was in the Organized directory, the old device directory and App Download Folder 2. The autoselect would select the ones that were in the lowest directory first. Then be able to say 'Autoselect least preferred directories'. It would be helpful to set up a list of directories that are prioritized, like this: Then, the next best directory would be the download folder (because a bunch were downloaded in sequence by author), then the other directories down the line. Ideally, you want to keep the ones in your organized archive before the others.
Now, you have a bunch of files that you've downloaded different ways, that are scattered throughout the download folders, but you want to make it as easy as possible to find the ones that aren't duplicated (say ones that were downloaded in sequence that were created by the same author in your download folder, as opposed to more random ones in the other directories). They all have unhelpful names like 104058666.pdf. Then you have a directory that is where you keep the ones you want to keep in an organized way (by subject/author/etc.).
Well, say you download a bunch of PDFs into the download folder, an app download folder and another app download folder, and maybe you have more that are copied over from an old device into another directory.