Sorry to read about your conundrum. I owned a custom knife in S90V and never had an issue with it. Like D2, we didn't want the edge to go flat dull, so asked for advice from the maker, become a friend in years following. Following the Crucible method, give the edge a good sharpening after using the blade well enough for it to start to pull. Seems in the next few rounds of sharpening there were less and less issues with chipping. In other words, just use the knife and don't worry too much.
Benchmade's been my favorite brand for more than ten years. Call it a growth spurt, albeit a painful one, there are a lot more production issues than ever was in past years. And frankly, although I don't care for Spyderco's offerings, they do seem to be more successful with their runs. There Is a pattern of off-centering, mixed with grind issues, and yes chipping. I read comments about many receiving flawless examples of the 940-1, but many also have theirs come out of the box on the other end...as described, that's a real problem.
I'm just a long-time enthusiast, so won't tell you what to do, but there Are other makers out there; some with issues of their own too, that use S90V (which has been around for many years...) Maybe it's held to a draw by Benchmade's superb customer Service. They are famous for fixing these production glitches. I know I've slowed way down on purchases. And have friends that have done the same. There's again a problem not openly discussed, but it's got to be hurting their bottom line.
Advice? Pick up a 940 from the regular catalog offerings. They're the same knife, just maybe simpler and not rushed to the market. There's a lot of us that own and love them. Good luck whatever you choose.