I am using KDE and I have different virtual desktops for different applications. For example, Dolphin is in virtual desktop number 4. If I open a video file, it launches in the same virtual desktop. I would like to move it to a different desktop automatically. I created a windows rule that always opens VLC in desktop number 6. Here's the rule: https://i.imgur.com/yGnfuVB.png.

This does move VLC to desktop number 6, but there's an icon for VLC in desktop number 4 as well. How do I make it so that VLC is in a single desktop instead of in both?

That is probably because you chose "Apply Initially", which only applies if you open vlc directly, not if you click on a link that will be opened in vlc. Try "Force" instead (haven't tested).

FWIW: this is a per application rule, not a window rule which applies to all windows.