Groups - loosing assigned groups

I have allways assigned groups to all my refs. Sometimes more than one. I now noticed 300 out of 1600 refs are unfiled!!

I realize this cannot be restored (or can it?) but how can I prevent this from happening again. In my back-up the same issue, probably because I backuped the faulted copy as well. So why are some refs removed from the groups and some not?is this becuase i used more than1 group for a single ref? 

How do you backup your library?