-Drebel.check_class_hash=true was introduced for this kind of cases. But you what you should actually check is why your client side classes are reloaded. JRebel reloads classes when the timestamp of the class file changes, or, if -Drebel.check_class_hash=true is set it will check for the hash in addition to timestamp.
So the very first thing to look for is when you make a single class, did the other classes' timestamps, that JRebel reloaded, change? Maybe IntelliJ's build for GWT just touches too many files during compile time? Or maybe you could just compile the single class, the one that you have actually changed.
One assumption that I have, is if the the above is not true, then there's GWT.create somewhere in your code that you're changing and it has to be re-run during make since otherwise the changes you have made wouldn't be propagated. This would only be triggered by the make procedure and JRebel doesn't trigger re-running GWT.create on its own. This is just an assumption, so please do not take it 100% seriously.
You could try contacting JRebel support as well.