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The plugin uses for restore the backup you select from the restore drop down box, field "Choose clone archive to install:", by default, the script selects the last archive from that list, so if your backup archive is somewhere inside the list you would need to select is manually!
I would advise to recheck your restore paths, specially the ftp restore path, if not i simply suggest to use the "Install file directly:" option instead of ftp on the Joomla.Cloner.php screen
If you still have problems, feel free to open a ticket and send us your ftp+mysql restore details and the backup to clone location
Ovidiu
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