What I can suggest you, firsthand, is to consider to manually copy /etc, /srv and /usr directories to /home, so next time you make a backup, you will have them there. But sometimes, the only working domain would be dom0, so you wouldn’t be able to reach backup, yet still you would have them in your home directory.
Where PKG is the list of packages from above, just the name (version not necessary). E.g.: qubes-core-qrexec-dom0-4.4.2-1.13.fc41.x86_64 becomes qubes-core-qrexec-dom0.
I’m sure there are better ways to do that but in dom0, you can use rpm --queryformat to get some information about your files, if you still have them. I.e.:
rpm --queryformat /etc/qubes-rpc/*
This is the list of potential packages to reinstall. I don’t know if it’s a good idea, though. You might try to just download the packages and select the files you want.
Another option to do that is to search the file name on Github (you need an account) or with a search engine. Then you have to use the git repo (and verify it) to get back the files…