After taking my lossless drives offline I ran an import. Despite checking "Fix broken links: Yes (protect network files)" Media Center removed all the files on one of the two lossless drives from the library.
Both drives are offline. It would make more sense to take all or none.
But it really should leave them all in the library as it used to and treat these as 'network drives'.
NOTE: I have had these drives offline frequently without files being removed from the library during import, this is a first thus bringing me to see it as a bug.