Hi,
I can confirm Roels answer. I have recently re-installed everything on my computer; Windows 7, Cubase 7.5, Halion 5 etc. I found out I was missing some sounds as well, mainly in the Halion 4 Factory set. I did as Roel wrote above, when windows asked what to do with the files that were identical, I chose skip.
I solved my problems after copying all VSTsounds from my 2 Halion DVDs that I got with Cubase 7. There were quite some libraries that were not on the Halion content dvd iso that you can download in the Cubase 7.5 section.
No everything works like a charm and I have total of 21 libraries and 5876 instruments in Halion 5.