The readme file explains the process: uninstall the old verson (your profiles and settings are preserved) and reinstall the new version.
It also has the change log.
With Comskip, if you’re using a newer version, you can set the comskip path and MCEBuddy won’t touch it in the upgrade process. I am pretty sure it also preserves your comskip.ini file from the builtin comskip during upgrades.
If you have overlaid HandbrakeCLI or FFMPEG with newer versions, you’ll have to re-apply your overlay.