If the FBI comes knocking on your door, you have already been tagged, and likely thoroughly investigated for something bad. Or more simply put: There is no good reason for the FBI to pay you a visit. She has every right to be "paranoid."
Conducting a background investigation on someone else applying for a security clearance is arguably a "good" (or at least, not-bad) reason for the FBI to pay you a visit. (Also, criminal investigations in which you are not a target may also be not-bad, depending on the exact circumstances.)
As far as I can tell the only details revealed by the FBI in this case is that they had some "documents" (without giving any context) for the author to review and answer questions about, and refused to share any details with her lawyer.
I'm not discounting that there are FBI agents who behave properly and politely without pushing the limits of legality, but I also believe there's plenty of evidence to suggest that there are plenty of agents who share none of those qualities (note that I'm not speculating on what fraction of agents are in each bucket, just that both are non-zero).
https://www.opm.gov/investigations/background-investigations...
If it's an ongoing investigation, having the lawyer there is a GOOD THING, because it becomes the lawyer's job to keep his client aware of the repercussions of doing anything to sabotage the investigation.