Editing in Sonar is how I handle that.

You can go back to BB or RB and select settings that allow you to do some things..... but they don't always yield the perfect results.

Another option is to use a drum synth and create the exact notes you want. I have used this as well. It takes a little bit of time to get the EQ right so it sounds like the same kit.

I have also been known to find the exact hit I need and copy and paste to where I want. The bad thing about the muting route as you have found is that the reverb tails and fades get muted and that makes it sound weird. That's a real pain on cymbal crashes or the reverberation of a tom's triplet ending.

You need to be able to think out of the box to get some things done properly.

You can find my music at:
www.herbhartley.com
Add nothing that adds nothing to the music.
You can make excuses or you can make progress but not both.

The magic you are looking for is in the work you are avoiding.