LiveChat 
Support 
Upgrading existing Joomla installation
Q. to my existing joomla installation Does Fantastico allow auto upgrades ?
Ans. Fantastico stores installation data within your account (below public_html). You’ll have to be compelled to make sure that you create correct package of your account before uploading that on our servers. You’ll also get the account transfer done from our staff as we will get this done quickly and you won’t loose any data from your account we would take care of your data transfer.
Mostly Webmasters choose to upgrade Joomla manually as upgrade from Fantastico overrides custom styles and navigation therefore you need to assure that you just take a full backup of your Joomla installation before upgrading from Fantastico.