I'm saddened to read of your experience. No polygraph operator has ever demonstrated the ability to detect polygraph countermeasures at better than chance levels of accuracy. There are no articles or book chapters in the polygraph literature on how to detect them. But that doesn't deter polygraphers from ruining careers with accusations of countermeasure use.

Unfortunately, I don't think your application will survive an accusation of countermeasure use -- however unfounded it may be -- by the FBI HQ polygraph unit. I know of no analagous instances where an applicant has successfully appealed. Making matters worse, the FBI's false accusation of countermeasure use may make it difficult for you to find employment with any federal agency that requires a security clearance.

Your FBI file is a permanent record, and this polygraph "failure" will follow you the rest of your life. At least to document the fact that you do not (through your silence) tacitly accept the countermeasure accusation, you will want to contest that accusation in writing (either now or upon official notification of the results).