Clearly a case for Special Agent Kujan, this mystery may be traced to Kaiser Soze directly. The mislabeled 6/7s were pretty easy to understand: Only the production knives have the model put on them, since a CQC7 can be an "A" or "B" model. Ernie sent the blades for the 6s to the same etcher, and unhandled, they probably looked just like the other blades he'd been doing, and so the etcher put the model on them. I'm pretty sure it wasn't because they were using production techniques, parts, and people to churn out 6s to reduce the backlog. Once discovered, the quality control checklist got a new step, so no more mix-ups on etching.
The double logos ti knives explanation doesn't hold up in the same way. The half moon Emerson hasn't been used since 1995 at the latest. Those knives couldn't have been logo'd with it in 1998 and then redone immediately afterward upon noticing a blemish. The logical explanation is: the blades were made pre-1995, and logo'd awaiting final construction; for whatever reason, they weren't put together until '98, at which time the new logos were in use; they were then re-beaded and correctly logo'd, inadvertently leaving behind the faint hm logo. The illogical thing is: why circulate a demonstrably inaccurate explanation? What possible blemish was trying to be hidden by this flimsy cover? I think only Soze knows for sure...