An articulated instrument is controllably movable between areas of different work space limits, such as when it is extendable out of and retractable into a guide tube. To avoid abrupt transitions in joint actuations as the joint moves between areas of different work space limits, a controller limits error feedback used to control its movement. To provide smooth joint control as the instrument moves between areas of different work space limits, the controller imposes barrier and ratcheting constraints on each directly actuatable joint of the instrument when the joint is commanded to cross between areas of different work space limits.