It's not an error. You need to do it before you chroot or you can't get to the real /etc. You are copying the resolv.conf used with the LiveCD boot to what will be your Gentoo install /etc. You don't run env-update until after you chroot.<snip>
1. copy resolv.conf 2. do whatever else 3. chroot 4 then env-update
Let me be clear. I copyied resolv.conf
Did that other stuff
chroot'd
ran env-update
Errored out and couldn't emerge sync.
Exited out
cp'd make.conf
re-chroot'd
re-ran env-update
Successful exit on that
am now running emerge sync
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