Questionnaires associated with an assessment can advance through workflow stages independently. Note that prior to version 4.1, questionnaires had to transition through workflow stages in unison. By default, questionnaires still advance through workflow stages together. Questionnaires all start in the first stage of a workflow ("Information Gathering," for example) and must reach the Terminal stage together. You can create custom templates that allow independent stage transitions, also known as branching.
Relationships with a set of standard workflow templates, including "Assessments with Branching," which supports independent stage transitions.