I have file conflicts while updating my system

Possibly - but I would prefer to use manjaro-tools to create a Manjaro ISO.

And yes you can create an ISO from your running system - it requires som manual doing but possible.

Basically you need to

  1. install the manjaro-tools-iso package
  2. initialize iso-profiles repo
  3. copy the folder /etc/manjaro-tools to your ~/.coinfig
  4. create a file in ~/.config/manjaro-tools/iso-profiles.conf with content
    run_dir $HOME/iso-profiles
    
  5. copy the content of your user’s home to the iso-profile’s desktop-overlay/etc/skel
  6. build the profile
    buildiso -p profile-name
    

Your error comes from having installed a system wide python package using sudo pip.

Remove the package using sudo pip - Reinstall it using the package manager

Then rerun your update