Ppa-desktop-client deleted all files // flatpak safe?

Perhaps you can also use

add-apt-repository ppa:nextcloud-devs/client
sudo apt-get update
sudo apt install nextcloud-client (nextcloud-desktop)

I think the official package for all linux users is the Appimage.
Flatpak and Snap are a little bit the windows way :wink:

Years ago nobody needed the newest version of software and the distributor e.g. Debian patched the software and build the packages.