Mit folgendem Code könnt ihr eine CheckBoxList aus eurem Repeater auslesen:
  foreach (Control ri in rep.Controls){
           if(ri is RepeaterItem)
           foreach(Control control in ((RepeaterItem)ri).Controls)
           {
             if (control is CheckBoxList){
               foreach (ListItem item in ((CheckBoxList) control).Items){
                 if (item.Selected)
                   // do
               }
             }
           }
         }