the installer only knows fresh install.
Boot into F39
open a Terminal and enter the following commands:
sudo dnf upgrade --refresh
reboot
sudo dnf install dnf-plugin-system-upgrade ## only if you’d never upgraded before this way
sudo dnf system-upgrade download --releasever=40
sudo dnf system-upgrade download --releasever=40 --allowerasing ## only if previous command didn’t work properly
sudo dnf system-upgrade reboot
That’s my way to upgrade - did it since F30 and worked for me all the time.
See also: Upgrading Fedora Linux to a New Release :: Fedora Docs
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got it!
Probably there will be some delay before the upgrade process is offered to the users through the Software Center. I also prefer upgrading through the terminal though.