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It sounds like you are using the Live system - the entire operating system as Live system in a readonly mode. To make Fedora 29 persistent, you need to install it! When you fire up your Live system, start the installer!

(Another thing I can think of: In case you have installed Fedora, you need to remove the install media (detach the .iso from the virtual machine), so a reboot doesn't fire up the Live CD again).

Anyway, you should download Fedora exclusively from (and the project's mirrors). Use the workstation images, or workstation spins that feature other Desktop Environments, but I would assume Silverblue or Server is not what you are looking for. (Other than there is no server live image, you are forced to install it)