I have run across a similar issue and the only solution I came up with was deleting the entire crate from Serato DJ, then redragging the folder from the “Files” section of Serato DJ into the crates section. Serato seems to reread the folder and only put in the crate what is in the folder. Serato does a lot of things right and very well, but library management is not one of those things, IMO.
An issue I am having is dealing with a crate I made that wasn’t previously a folder from the files area. I made the crate first by putting tracks in the prepare window, and then selecting all those tracks and dragging them down into the crate area. Later, I moved some of those files around in my folder system, causing the corresponding songs to turn orange with the question mark. Clicking relocate lost files does not fix them in that crate, although they still appear in the smart crates I have set up by key and by BPM. GRRRR.
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