I don't know enough about your system, I'd recommend that you create an archive of both /etc and /var and store them safely on another system (..tar/cpio/dump etc).
This will allow you to carefully review everything and then you can selectively merge things later.
It's better to have them and not need them, then need them and not have them.
Do you SSH to this system? you may wish to at least retain the host keys.
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