I recently upgraded the Whonix-Workstation-17 template to the latest version using the Template Manager. However, I have multiple clones of the Whonix-Workstation template.
Since the Template Manager only provides an option to upgrade the base template, is there a way to in-place upgrade the cloned templates, or do I need to recreate all of them?
If I understand you correctly, you have upgraded the @commandline repository to the qubes-templates-community.
If that’s the case, I think you need to recreate your other templates because it’s not the same repository.
Is there no way to manually change the repository of these cloned templates and then upgrade them?
I don’t think so 
My solution would be to get the packages you installed in each of your templates( with .sls file and .top) , clone your new template and then use SALT to reinstall the packages in each new template you cloned.
I’m not sure I was very clear lol
This is what I do to make backups of my templates. I retrieve the packages installed in each template and then use salt to restore the new templates. There are many tutorials in the forum on this subject.
edit: this could help you for salt 
https://doc.qubes-os.org/en/latest/user/advanced-topics/salt.html#example-of-configuring-templates-from-dom0
What exactly do you mean by “in-place upgrade”?
Are you referring to upgrading from, say, 4.1 to 4.2 Qubes repositories, or upgrading from Whonix 16 to 17?
Both upgrades are easy, but my issue is different. In the Qubes Template Manager, there was a newer version of Whonix Workstation 17 in the Qubes community templates repository. The original Whonix Workstation 17 is in the @commandline repository, but it can be upgraded using the community templates version. I upgraded the base template successfully, but there is no way to upgrade the cloned templates. I was asking if it was possible to upgrade these cloned templates in-place, without recreating them.
The templates are simply rebuilt with the latest packages.
Most features are added through packages updates. The only feature I can think of that isn’t added this way by default is the new user isolation with Sysmaint. If you want it, you can enable it by installing a package:
Really? That’s a bummer. The first thing I did was remove the sysmaint user split and set up passwordless root, so it sounds like upgrading the template was a waste of time. :-/
@DVM so it’s the only difference between the @commanline repository and the qubes-templates-community for whonix-workstation-17 ?? i’m not sure to understand
And if the whonix-worksation template is upgraded with the qubes-templates-community repository, the clones will still be updated via the @commandline repository, right?
edit: My bad, just checking “Community Templates” in the “Updates” tab of “Qubes Global Settings” and updates will be done automatically! i am wrong?
@commandline does not refer to a repository. Rather, it indicates that the template was installed via the command line using tools such as dnf or rpm. It is most likely that their .rpm package was installed by the Qubes installer.
It asks you to upgrade because the template was built more recently and has a more updated set of packages, as indicated by its version. However, it is not necessary to do so if you update it with Qubes Update.