TOFERGREGG  Yes, it seems that there is still a problem for some users. It normally works if you double-click on the site name _twice_, and you close iWeb between each click.  
(Version 2.4b)

TOFERGREGG  Hi there -- I am sorry to hear of your troubles. Please email me at tofer@mistergregg.com and I can help you troubleshoot the problem. It should be a simple fix, and I doubt your websites are gone.  
(Version 2.2)

TOFERGREGG  Hi there -- I am the developer of iWebSites, and I am very sorry the program has deleted your site. I don't know why that would happen, unless iWeb was running when you used iWebSites (although iWebSites does warn you if this is the case). You may wish to check in the trash to see if your site is there. Please e-mail me directly at tofer@mistergregg.com and I can see what might be able to be done about it.  
(Version 1.0)