Routes are not removed from the schedules automatically ever.
The only exception to this is the activation of the noise regulation limits, if the plane does not meet the limits. (Several messages are sent about this before it happens..)
The route can be unscheduled by player's actions from three reasons: 1) editing the route so that the flight times or fleet group changes, 2) using the "remove flight from schedule" button/function at schedule page (or clearing the whole a/c schedule), 3) closing the route.
Having the route inactive and losing the slots will not unschedule it but just mark as having no slots (which can be then reactivated by just edit-save combination at the route editor since it re-buys the slots).