diff --git a/tools/process_config.sh b/tools/process_config.sh
index a9aaf143182..6d1be7e55a9 100755
--- a/tools/process_config.sh
+++ b/tools/process_config.sh
@@ -56,6 +56,8 @@ process_file() {
                 exit 1
             fi
         else
+            local key_config="$(echo "$line" | cut -d= -f1)="
+            sed -i "/$key_config/d" $output_file
             echo "$line" >> $output_file
         fi
     done < "$input_file"