Is it possible to mass copy files from one qube to others without copying to dom0?

[unman]

Is there a way to run a series of commands in Dom0 to copy files and folders from one Qube to another without user intervention, and without copying files to Dom0?

Of course.
qvm-copy-to-vm is indeed deprecated, but you can replace it’s
functionality in this case using a policy:
qubes.Filecopy * SOURCE @anyvm allow target=TARGET

This policy will mean that any instance of qvm-copy will be allowed
and the files transferred to TARGET without user intervention.

Armed with that, you can then run qvm-run SOURCE 'cp DIRECTORY' from
dom0.
Remove the policy when done.

The risk here is that while this policy is in place any files may be
transferred from SOURCE - you should probably prune QubesIncoming/SOURCE
to make sure that nothing untoward has been transferred.

Alternatives are to use a shared folder - noted
here - or a utility like
syncthing - packaged for Qubes here
Either of these will allow for transfers over qrexec, controlled by a
Qubes policy file, and are callable from dom0.

I never presume to speak for the Qubes team. When I comment in the Forum or in the mailing lists I speak for myself.