I've been seeing alot of this when I try to get projects by label, date or version using VSS command line:

Project $[suchandsuch] has been destroyed, and cannot be rebuilt.
Continue anyway?(Y/N)y

There is a hot fix available for this bug!  http://support.microsoft.com/?id=887604

In addition, I have gotten used to the message :

"version not found"

when trying to get by label using VSS command line.

The hot fix for this bug is located at: http://support.microsoft.com/default.aspx?scid=kb;EN-US;837417

Your database must be upgraded to the most up to date version as well. 

"To determine if your Visual SourceSafe 6.0 database has been upgraded to the new database format, check your Visual SourceSafe data directory for a file named Crcs.dat and a subdirectory named Labels."  http://support.microsoft.com/kb/153925/EN-US/

The latest service pack (6) for Visual Studio is located:.

http://support.microsoft.com/?scid=kb;en-us;197050&spid=3036&sid=global

all that being said, I have verified my database to contain the listed file and directory and applied service pack 6.  ss command line still will not retrieve files in sub directories that are labeled with the supplied label.  It's quite annoying.  I will try to get the hot fix applied next week.  If that fixes the problem, I will update this post.