Use Ctrl S (ie saving metadata back to the file or to its sidecar XMP file) if you routinely open the files in another program. For example, if you often want to open files directly from Bridge or directly in Photoshop, then save the metadata out either automatically or with Ctrl S.
Otherwise, as Jon said, backup your catalogue regularly and rely on it. All your metadata is there - it isn't all in the XMP.
So think of the XMP files as being mainly for communication with other programs, not backup.
John