If you go to your online organizer (click My Library), and select All Photos and Video in your Library, do your pictures show there?
We do not delete photos from user accounts, so I wonder if there is another explanation. Were the images in an album, which you deleted? When deleting albums, one sees a checkbox asking the user if he or she also wants to delete the photos in the album from the main Library too. This is not selected by default, but is it possible you checked this box when deleting am album?