Wine data is stored within the
WINEPREFIX directory, usually at
/home/$USER/.wine/ unless otherwise defined. Such directories are not deleted during the upgrade process. (You'd have to physically delete the directory yourself)
You don't need to worry about that data being 'lost' when you update Wine versions.
However, if you really are concerned about that, make a copy of your Wine prefix elsewhere called "wine_backup" or similar with
cp -r ~/.wine ~/.winebackup first - this way you can always restore the data if the
.wine directory goes away by doing
rm -rf ~/.wine && cp -r ~/.winebackup ~/.wine (which will remove a 'bad' wineprefix if it exists and restore the backup.
You may wish to read up on the WineHQ guide for Ubuntu on how to deploy newer Wine (latest stable) on your system. They maintain a repository now for Ubuntu versions of the latest Wine. (I'm on my phone, I can't copy in the data from that site now, but I will at my earliest convenience after work this evening - assuming I remember)