The file in \Data\Default Resources\ will be updated if there are changes.
Your custom file that you save in \Data\Custom Resources\ will not be updated and will be the file that MC continues to use.
So...
When installing new versions of MC, even though the file might not have been changed, the installer will still write a new copy of the file, removing any edits you may have made. With an edted copy in the custom resources folder, you don't need to worry about that any longer.
If something stops working, or perhaps you're not seeing a new feature, all you need to remember is that your first task before crying 'foul' is to manually sync the two pdt files.