I can confirm that upgrading goes through without breaking stuff if you change bookworm to trixie in
/etc/apt/sources.list.d/debian.list
/etc/apt/sources.list.d/qubes-r4.list
My template might be a debian-minimal which I kali-fied, not sure about that. So, there might not be a debian.list in your template. Also, I have a file on_hold in /root/ which looks like this
python3-qubesdb
python3-qubesimgconverter
qubes-core-admin-client
qubes-core-agent
qubes-core-agent-dbgsym
qubes-core-agent-dom0-updates
qubes-core-agent-nautilus
qubes-core-agent-network-manager
qubes-core-agent-networking
qubes-core-agent-passwordless-root
qubes-core-agent-thunar
qubes-core-qrexec
qubes-core-qrexec-dbgsym
qubes-gpg-split
qubes-gui-agent
qubes-img-converter
qubes-input-proxy-sender
qubes-mgmt-salt-vm-connector
qubes-pdf-converter
qubes-usb-proxy
qubes-vm-dependencies
and can be used like this
apt-mark unhold $(cat on_hold)
apt-mark hold $(cat on_hold)
apt-mark showhold
I usually update the kali template from the command line with the aforementioned packages on hold. When apt returns issues I don’t update and make a backup of the template instead.