So, in addition to making sure you copy all the files that have changed since you last backed up, you should make a note of those.
As you can see, CleanMyMac X does a lot more than just clear out junk files before you backup your Mac. Before you backup, however, you should take steps to remove the junk and clutter from your Mac. It removes gigabytes of temporary files and other junk to optimize your whole system. If you are facing the slow performance of your Mac due to the upgrade, there is an app that could help.