The so-called gas plants trial will continue, after Justice Lipson rejected a motion to throw out the remaining charges against two Liberal aides to former premier Dalton McGuinty.
David Livingston and Laura Miller are accused of destroying documents related to the Liberal government's decision to scrap two gas plants ahead of the 2011 election.
Last week, the Crown dropped a charge of breach of trust.
The defence had requested an acquittal, but the judge has denied that request.