I have previously used click-once deployment to publish multiple windows applications in Visual Studios .Net 2005. Periodically, I had to choose a new certificate from the certificate store in Visual Studios (Select a Certificate window) when the old certificate expired. This has been no problem until recently. Now when I open the "Select a Certificate window" there are no certificates to display. It looks like some type of download within our office may have emptied my certificate store. When I look under content through Internet Explorer, there are no certificates available.

Has anyone seen something like this before? How do you recover certificates in INternet Explorer?

This is a common problem .If you want to do edit any of the dlls of Click once this expiration will make few issue that you can solve like
http://blogs.msdn.com/danielma/archive/2007/03/19/clickonce-and-expired-certificates.aspx
Else you recreate a new certificate and try to host it in your system.

Regards,
Pramod