I heard that changes made to the system partitions (like manually installed packages) are lost during update. There are actually two efi and two root partitions on the Deck, only one of each actually being in use, so my theory is that the update actually just upgrades the other partitions (the ones not in use) and then tells the bootloader to load those instead of the unupdated one. That would mean that after each update, the Deck actually switches to a different partition for the OS.

Since I'm not too keen on this happening and losing my manually installed packages, here's a question: Can the updates be avoided entirely by manually updating packages with "sudo pacman -Syu", or would some important updates be missed by that method?