Upadted from Control panel GUI 4 reboots later all is well It was scary at first reboot black screen then with each successfull boot getting back a little more than the last. After 4th reboot everthing was restored! Stock HP N54L with 6 drive bios update orig drive on top in removable bay only 2 drives in bottom 3tb Raid1. I'm happy!!! Love this stuff! Any Questions?
Update!! After further investigation had to shut down Re-indexing service and delete the cache for it. Look around on this site for how to do this! There are many links on this site for doing this follow one you feel applies to your situation. I also had to re-apply some permissions (not all) and re-install some packages (again not all) but no data was lost. I have most of my data on a second volume this may be why, not sure. All in all not too much time to get around all the other stuff. All is well now!