Which VIs are missing? It could be possible that you had some toolkit installed for 7.1 but you dont have it installed for 8.x.
Dependencies lists VIs used by VIs in the project that are not already in the project. So it makes sense that LV would remove these VIs from this list if they are added to the project.
Have you tried refreshing the dependencies list by right-clicking on it and selecting Refresh?
Regards,
Chetan K
Application Engineering
National Instruments