Hi Brett,
high variance of 9999 means that robot_localization would "ignore" that entry. I am not aware of this, but is -1 covariance make robot_localization ignoring the corresponding value? Note also that you can disable visual odometry to publish null odom topic by setting parameter "
publish_null_when_lost" to false for rgbd_odometry/stereo_odometry node.
If you have another source of pose estimation, it would be used to continue to estimate the filtered pose. If I take Google Tango for example (visual inertial odometry): if we obstruct the fish eye camera, the filter still estimate the position of Tango using the IMU for ~1 second, then it stops (as it would continuously drift using only IMU) and the filter should be reinitialized when features can be extracted from the camera again. Not sure how to achieve a similar behavior with robot_localization, maybe by blocking all inputs to robot_localization when visual odometry is lost. Thus to answer your main question, it is indeed no.
cheers,
Mathieu