Sadly there's nothing we can do, since the error comes from Joomla itself.
The only advice we can provide is to downgrade to Joomla 3.4.6 until a proper fix has been published.
However that's a quite rare bug, it happens when the upload process takes too long and MySQL closes the connection.
You can try to lower the part size for the FTP upload, that should speed up things and prevent the database from closing the connection. It's a long shot, but it's worth trying.
Davide Tampellini
Developer and Support Staff
🇮🇹Italian: native 🇬🇧English: good • 🕐 My time zone is Europe / Rome (UTC +1)
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!