That was one aspect of the auditing, but they also sent audit notices to random small and medium businesses who were not volume license customers. Basically fishing for license violations, which obviously were very common (and usually unintentional) back in the 90s and early 2000s. Things like installing windows XP or Office on multiple machines without buying extra licenses.

AFAIK it was mainly a scare tactic to pressure companies into compliance and mostly just involved scary looking letters from a Microsoft-hired law firm.