It doesn't really even sound like they "missed" it. I.e. from the article:
> The judge said the CDC, along with all other Department of Health and Human Services agencies, had adopted a National Archives protocol known as Capstone that calls for senior officials’ emails to be preserved permanently and sets retention periods of between three and seven years for messages in the accounts of lower-level employees. CDC maintained it only signed on to part of the Capstone approach, but Contreras said the agency appeared to have embraced the whole plan and then abandoned part of it without permission.
That is, there seems to be enough ambiguity there, especially in that last sentence, suggesting the CDC reasonably thought they were acting lawfully.
Not reported or not caught in spot checks (audits). You'd need a list of "lower level" (whatever that means) employees who had left more than 90 days prior to catch this.
Also, many audits are somewhat optimistic in their approach. Ask for some portion of the archives. See a few hundred employees here (perhaps all GS-13 and up) who left 4 years or so ago and are still in the archives. Great! They don't dig into who the employees are to notice that lower ranked employee emails are gone and everything looks compliant. This isn't the only audit they need to do this week so this is as far as they go.
Presumably CDC's records retentions policies go back many years, and the GRS 6.1 Capstone rules were promulgated in 2019, so (a) the policy discrepancy is pretty recent and (b) the douchebags-of-liberty† challenging it only had an opportunity to do so after the previous Republican administration left office --- they themselves being right-wing partisans.
