After Restore I have duplicates with extension ".backup.20131121"

This is because 'Backup files on restore' in Options was enabled. This is default setting to prevent overriding files on restore.

If you don't need them any more you can delete those files. Open a terminal and run:
find /path/to/files -regextype posix-basic -regex ".*\.backup\.[[:digit:]]\{8\}"

Check if this correctly listed all those files you want to delete and than run:
find /path/to/files -regextype posix-basic -regex ".*\.backup\.[[:digit:]]\{8\}" -delete