Duplicate files · Scanning and Auto-scan
Why does the duplicate scan say it covered only part of my files?
Short answer: On a very large collection, one scan covers as much as it sensibly can and says so instead of implying it checked everything. The duplicates shown are real: clean the ones you want, then scan again to cover more.
On a very large collection of files, one scan covers as much as it sensibly can and then tells you so, rather than pretending it looked at everything. The status line marks the result as partial, and hovering over it explains how much was covered.
The duplicates shown are real — clean the ones you want, then click Scan now again to cover more. Repeating the scan without clearing anything tends to look at the same files again, so tidying up between scans is what moves it forward.
This limit exists so a scan never uses an unreasonable amount of memory, especially on Macs with less of it.