VST Content folders-can someone explain please?

Its to do with the Halion Library manager app. On the managed and installed tab I notice a warning which indicated that some of the content had duplicates. I removed the duplicates but when I opened cubase it was telling me a lot of the content was missing and it was asking me to locate the files -which where on the trash. One by one I put the sounds back in the designated VST sound folder. What I find very confusing is the the fact that there are two VST content files-one in the user library and one in the Hard drive library. Why can’t they all be in one file?