Sounds like they didn't even have perfect records of what software was deployed while they were trying to resuscitate the spacecraft? Because software deployed over the years to the same limited memory overwrote previous versions of software. Eventually they managed to get that memory dump (from a fail-safe and/or plain luck) which probably gave them a clearer picture of what they were dealing with.
Apparently they don't have a lot of the details either, and may not even be allowed to make some of what they have public? Note the line at the bottom of the presentation: "This document has been reviewed and determined not to contain export controlled CUI."
