rockm

"I originally wanted to remove the trunk on the left, but was afraid of having a big nasty scar."

Well, you either have a scar (which can be a plus when worked in the way Jim has illustrated) or you can have a big funny looking jin. for what it's worth, most old collected boxwood have drastic pruning that needs to be done, often resulting in a scar. Since boxwood is so dense, it is one of the few broadleaved trees that can handle deadwood treatments like a conifer. The wood does not rot and carves up well, if not easily.

ALL of the big (over 4 inch diameter) boxwood bonsai I've seen (and I have one with a 4" nebari myself) have deadwood treatments. My tree has a significant portion of deadwood on it's backside that's been carved to resemble not a windswept piece of driftwood, but an insect eaten, water damaged weatherbeaten stump--the wood is still VERY solid after six years.

I'd cut the long jin on yours back to about six inches, get out a Dremel (and several NEW grinding bits--you will need more than one, as the wood will dull them pretty quickly) and go to work. If you've never worked a deadwood treatment on a bonsai, I would practice carving, on a piece of separate deadwood, or old lumber before working on the tree. See what techniques work--drilling into the wood, then thinning it from the outside can create irregular weathered loooking "see through" knot holes, for instance. Of you can create irregular circular holes in the wood, along with crevices, etc. with smaller bits of varying sizes....

Or you could save the jin for carving work in a professional workshop. This could take some time if you haven't got access to such programs though.