Try this:
- create a folder containing two files: a and b
- in the folder, search for all files (Ctrl-F, Ctrl-F): a and b are found
- leave the Find window open
- outside the Find window, remove file a
- go back to the Find Window showing a and b
- do "Refine - Intersect with Found Items" (Ctrl-I)
Now file a is still shown, along with b.

I wanted to find what files shown in the list (which I filtered manually using Hide) still existed.

On second thought, I think I understand what happens. It seems that the Refine functions do not scan the disk for files, but rather apply the settings to the already found files. Maybe that makes sense. I guess I will have to rescan (Find Now) and Hide again. Or intersect with files containing a text that occurs in every file (such as the regex "."), which just ignores deleted files.

As a side note, the documentation says: "you can search in already found files (values in the Named and Look in boxes are ignored)." That appears to be not completely true: the Named value is applied, and right so. Please fix the documentation.