Project record level security is somewhat different than the account record level security. When a query is updated/changed that is being used on a user record for project security the results of the changed/updated query are not picked up by the user unless you follow the steps in KB Article 111508. I have not experienced this awkwardness with the account record level security. The application of this is in expense management where we have decided to allow users to code their credit card transactions with account codes and project codes. Make it so project security is similar to account security so the steps in KB article 111508 are not necessary for the user to pick the new query results.