Have you edited any files in /etc ?? The ones that will possibly get updated you probably haven't touched. It won't overwrite files like /etc/resolv.conf or /etc/hostname. It will often want to replace /etc/make.conf, for example.
Again, when you run etc-update, it will *LIST* all of the files it wants to update. You could probably 'cat' that list to a file too.
Somehow it managed to overwrite my /etc/fstab which I wasn't to happy about.
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