Previously, we installed its contents in a way that made pacman not aware of the files (using VBoxManage extpack install ... from an install script). To mitigate issues during upgrade, you can use one of the following methods:

• Uninstall virtualbox-ext-vnc before upgrading the system, then installing it again.
• Run VBoxManage extpack uninstall 'VNC' as root before upgrading the system.
• Instruct pacman once to overwrite the existing files:

pacman -Syu --overwrite '/usr/lib/virtualbox/ExtensionPacks/VNC/*'