I'm not sure what kind of polygraph the OP is referring to but if they had to take either a counterintelligence (CI) poly or a 'lifestyle' poly as part of a full scope examination etc., having some sort of partial memory due to a blackout and 'holding back' would probably show up as some form of deception. This happens to people who do not have drinking problems or blackouts when they get quizzed on sensitive aspects of their lives - especially past sexual behavior.
It helps to know the purpose and scope of the polygraph. Many people try to hold back information during these examinations as they mistakenly believe certain sexual behavior or drug use will somehow exclude them from employment or security clearance (it depends).