Hi Rob,
It's hard to say as to why you cannot find your VIs- what are some of the VIs that are missing? Let's try to narrow down the problem. Are these VIs used with any hardware or driver? If so what driver? Are these VIs ones that you have made? When you install a new version of LabVIEW, you need to make sure that your drivers are updated to have support for the latest install of LabVIEW. Furthermore, LabVIEW has certain directories that are searched for when trying to find VIs - make sure to include the directory as to where your VIs have been saved in the past.
I hope this helps
Regards,
Nadim
Applications Engineering
National Instruments