Create a hidden directory in your home folder named .sysconfs
In here, make copies of modified system files, such as the .conf files found under /etc/default, /etc/pacman, fstab, crypttab, /usr/share/alsa-card-profile/mixer/paths, /etc/X11/, /etc/systemd/, and so on…
This way you can more comfortably switch to the new .pacnew versions at your own discretion and use your custom modified files in ~/.sysconfs/ as a reference to anything you might need to add / insert again.