Can I use Fantastico's script to upgrade to the latest XOOPS version?

It is NOT advised to upgrade your XOOPS instalation through Fantastico's upgrade script because the script does more than that, it also deletes the existing modules and existing themes from the server leaving just the SQL entries of them.
Even so you should be safe as Fantastico does a backup of your XOOPS instalation before running the script so all you have to do is restore missing modules & themes.

This Q&A was found on XOOPS Web Application System : https://xoops.org/modules/smartfaq/faq.php?faqid=665