It depends what was in your 'index.html' files.
If each 'index.html' file contained no custom content and your galleries did not use galleryURL or baseURL configuration options, then you can replace the missing 'index.html' files with the stock version which comes in the SimpleViewer-Pro download package ('simpleviewer_pro_231/web/index.html'). The only thing you may have to change is the backgroundColor configuration option for each gallery.