Paul, it is not normal you are loosing instruments.
With what you propose to do you will not recover lost instrumets
I had quite the same issue but the library was not missing any instrument ; instuments had damadged files.
I had quite a few crashes, messages from eLC saying I had instruments that was not autorized !!!!!!
I hope that eLC will fix this message saying which instrument is damadged ;))))))))))) that will save a lot of time in debugging the problem.
The only solution was to erase all my libs and copy them back from a backup
I did that last week end, now how can I find out if my backup has all the upgrades ?
VSL you do need a Software and Instruments update central program that could determine what is not updated, like the one of Native Instruments or like the one from Apple
Thanks in advance
Best
Cyril