As I recall Safari was notorious for caching the CSS files of a site, so it's possible WebKit behaves that way.
I've taken to minimizing the CSS code and keeping it in the Custom HTML Prompt action. My Minify/Unminify CSS/JS Files makes it easy to work with the unminified files while you're testing before minimizing for production.
So I've never experienced an issue with WebKit CSS caching.
I'll also note that I have sometimes found it prudent to click outside an Execute a [Script] action to make sure Keyboard Maestro digests my edits before I test them. But since I trimmed down my plist file, I haven't had as much trouble with this.
So it may not be caching but a delay in processing the changes back to the plist file in that case. No idea.