As someone who's managed funds for others and been through regulatory examinations, I can tell you they know pretty much everything.
When I got examined, I got a few weeks notice and they had a team spend nearly a week at my place. They got every statement, communication, document and file - both electronic and paper - that existed on my end. Then they contacted my accountant, auditor, bank, broker, randomly selected clients and everyone else that had any knowledge of my fund and got every document they could obtain DIRECTLY FROM THEM. If anything was a penny different, it was chased down and explained to their satisfaction. For all the ponzi schemes and others that have gotten away with fraud over the years - they were not fully examined by a regulatory authority.
I'm not sure when Karen was examined before, but if anything was amiss they would have caught it. Exams are not every year and not even regular. Much depends on your size and scope and other factors, but I think the goal is to examine everyone on average about every 5-7 years.
They will also not disclose everything in a briefing doc. It's just enough to establish misconduct and illustrate the level of deception that took place for the record.
I don't know Karen and I haven't really followed her except for some of what I've read here. I can tell you that most people that run funds that get involved in this kind of activity had a loss and started fudging to cover the loss with the intention of squaring things up once the funds were recouped. If you never make the money back, the hole gets deeper. And if the SEC/NFA shows up for an exam, it's over. Even if she fully recovered, they would have discovered the fraudulent reporting on her next exam. I'm not sure if this was her first exam or not, but if you have been through it once you know there is no way you could get away with anything.