A comparison is being made between your local copy of a file and the version of the file on the master Web or in the source control library. This occurs if you choose the Compare to Master Web command or if your project is under source control and you choose the Compare Versions command. This comparison will show differences between the two files and allow you to choose which version you want to save. However, the local copy of your file can't be found. The file may still be listed locally, but has been deleted. The comparison can't be made.
For more information, see Managing Web Projects or Working with Multiple Developers and your Microsoft® Visual SourceSafe™ documentation.