Microsoft Knowledge Base Article 263027 contains the following summary:
When you install Remote Installation Service (RIS) on a computer, you also set up Single Instance Storage (SIS) on a volume of the hard disk drive. SIS reduces the amount of space in a volume that data uses by removing duplicate files and placing them in a common store directory (\Sis Common Store), which is a hidden directory in the root directory of the volume. When you run Risetup.exe to complete the installation of RIS, you choose an NTFS file system volume on which to store your images. You install the SIS filter on this volume.
When you restore a volume that is managed by SIS, you must follow specific steps to prevent corruption of the data you are restoring. Also, because SIS manages the entire volume, not just the RIS directory structure, SIS will manage any data that you place on this volume.
Note: To successfully restore a SIS-managed volume, the SIS/Groveler must be running and attached to the volume to which you are restoring data. If it is not, any non-SIS-linked files will still be accessible, but SIS-linked files will not be accessible, and they will appear to be corrupted. The name and size of a SIS-linked file will appear as normal. However, the file will be a zero-length file because it will not have access to the data it should contain.