If you fail an FBI polygraph examination, you can expect that your results will be shared with DoD, if not immediately, then at the latest when your security clearance comes up for a periodic review. A National Agency Check will then show that you have an FBI file. Your file will be requested for review by DoD adjudicators, and it will show that you failed the polygraph, something considered by adjudicators as being highly derogatory.

Your safest bet is to decline the polygraph and continue in work that doesn't require you to consent to having your honest and integrity assessed based on such pseudoscientific quackery.

I don't know what the odds are of keeping one's DoD security clearance after failing an FBI counterintelligence-scope polygraph examination. I expect that a variety of factors would be taken into account. I do know of an army reserve officer who failed the CI portion of an FBI pre-employment polygraph examination but was ultimately able to keep his DoD security clearance. By contrast, in my case, based on a wrongly failed FBI pre-employment polygraph, the army adjudicator who revoked my security clearance speculated (in writing): "Could subject be the operative in an international spy ring or a courier for a drug cartel?"