I just spent a good time getting my backuped templates from Qubes 3 to work in 
Qubes 4 RC3. I'm posting here what I did (roughly) to get it work, in the hope 
it can help somebody.

After running qvm-backup-restore, starts a terminal for your VM:

$ qvm-run mytemplate gnome-terminal

In the VM, 

- Rename /etc/apt/sources.list.d/qubes-r3.list to 
- Replace mention of "3.2" to "4.0" qubes-r4.list

Now we will import the new GPG keys used to sign the packages.

- Start one of the official template:

 $ qvm-run debian-8 gnome-terminal

In the debian-8 VM:

$ apt-ket exportall > /tmp/keys.txt
$ qvm-copy-to-vm /tmp/keys.txt

Choose "mytemplate" as destination.

In the mytemplate VM:

$ apt-key import ~/QubesIncoming/debian-8/keys.txt

Now enable networking in the mytemplate settings by specifying sys-net as a 
network VM.

Updates the packages:

$ apt-get update
$ apt-get upgrade

When prompted, choose to use the qubes-r4.list from the maintainer (or merge 

Disable network in the mytemplate VM.

Now the proxy updates should work again.

Good luck.

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