The preferable way to update, is indeed to always please remove the previous NodeCanvas installation folder and re-install the new version anew.
Unfortunately, packages imported from the Asset Store does not use NuGet or the Unity Package Manager (which might or might not be able to handle file changes/renames) and hopefully Unity will update the Asset Store packages to using the Package Manager (or another better way) in the future, but right now all package imported from the Asset Store can not handle this, thus a fresh re-install is always preferred.
Thank you.
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