When removing duplicates, RJL System Cleaner keeps the oldest copy of each file (the one with the earliest last-modified date) and removes the newer copies.
The logic is straightforward: the oldest copy is most likely to be the "original" that was later copied or downloaded again. The newer copies are the duplicates.
Before removing any duplicates, the app shows a confirmation dialog listing how many files will be removed and how much space will be freed. The original files are clearly identified so you know exactly what is being kept.
If the Recycle Bin option is enabled in Settings, removed duplicates go to your Recycle Bin instead of being permanently deleted, so you can recover them if needed.