In 4.1, you would add this to dom0’s /etc/qubes/policy.d/30-user.policy:
qubes.Filecopy * srcvm destvm allow
In 4.0, if I remember correctly, you would add this to dom0’s /etc/qubes-rpc/policy/qubes.Filecopy (or create it if it doesn’t exist):
srcvm destvm allow
In srcvm, you can then run qvm-copy-to-vm destvm file1 file2
without a prompt.