"But seriously, this isn't FBI agents threatening her (although trying to bypass ones lawyer is certainly unethical). This is FBI agents trying to contact her for whatever reason, that is not a threat from the FBI though."

This is the crux of our disagreement and where I'm not totally disagreeing. We both say in various comments they might just want to talk to her. So, at this point, it can't be considered a threat with any certainty.

Given how they work, though, it's reasonable to consider it a probable threat if they (a) claim they want help, (b) want no lawyer present, and (c) [important] haven't offered or accepted immunity (at least NDA) for whatever goes on. The defense attorney on Don't Talk to Police mentioned that last one in case of IRS. "They just want to talk and not arrest/convict? Ask for immunity for whatever comes up. They left? That figures."

So, she shouldn't have fled. We have too little information to know if they intend to threaten or just get assistance. Yet, if they have malicious intent, they often don't do it the way they did you. Many of them gently lure a person in to do their own social engineering to connect remaining dots or get the golden confession for fast trial. Then, the crazy shit starts. This happens so much it should be a top consideration if they call you being nice.

So, the real question is, how does one assess at this point whether it's malicious or benign? It's an open question unfortunately. I'd consider going straight to the FBI field office with my lawyer to talk to an agent. We'd record the conversation. If it's questioning about me, I'd ask for termination of that line of questioning or immunity for anything involving me. If they won't do either, I leave and then treat them as a threat. I'd definitely get someone to talk to them first just to see how they act, though, before considering leaving.