To properly update your Proxmox VE server, you can use the CLI. Login to the web GUI and click on your Proxmox VE node. Click on the Shell button on the right side of the screen. In the shell, type in:

apt update

Next, type in:

apt dist-upgrade

If you are asked if you want to download all the packages, press y and press the Enter key. Updates will now download and install.

It is recommended to use dist-upgrade over upgrade as dist-upgrade will remove packages in order to satisfy dependencies. It is possible to have a broken system due to incompatible package dependencies.