restart (or reload the config of) Eclipse-CS programmatically
The Checkstyle Preferences page contains in the top right corner a small refresh button. Hit the button after you modified your checkstyle.xml or suppressions.xml and the new configuration will be used.
(source: rolf-engelhard.de)
Reference: http://rolf-engelhard.de/2012/11/clearing-checkstyles-cache-in-eclipse
I've been struggling with this eclipse-cs shortcoming for years, and so far I am convinced that it truly isn't possible. You'd have to add this feature to the eclipse-cs code yourself, so it seems.
Sorry for the bleak outlook. "Cannot do" isn't really what you want for an answer, but it may still save some people who google for a solution some time.