I tried to remove the “old” RPM Fusion repos and then reinstall, but that didn’t work. Terminal output was that ffmpeg and ffmpeg-libs were unavaliable.
To fix what I broke, I rolled back to my previous version:
$ rpm-ostree rollback
I checked on ffmpeg and I am running the latest version, so all good for now.
Side-note, as I guess may be related and you still have that “harder” setup: You can simplify rpmfusion updates, like to Fedora 36 a lot, so you don’t need to uninstall and reinstall the rpmfusion repos etc. (That may also fix your upgrade issue there.)
Thank you @rugk!! I will try it.
I had to modify the code from Fedora Discussion so it works for Fedora Silverblue 36 users who upgraded from 35.
Before you run the command, confirm the version of the RPM Fusion repos you need to uninstall by running:
rpm-ostree status
Once I did that, I knew how to modify this code before running it in the terminal:
rpm-ostree update \
--uninstall rpmfusion-free-release-36-0.2.noarch \
--uninstall rpmfusion-nonfree-release-36-0.2.noarch \
--install rpmfusion-free-release \
--install rpmfusion-nonfree-release
After a reboot, this cleared up the issue with RPM Fusion repo updates in GNOME Software.
I was able to fix my issue following comment #24, here:
https://bugzilla.redhat.com/show_bug.cgi?id=2083715
That fixed one problem for me, but now I have 2088878 – Silverblue: Failed to create file ?/var/run/dnf-metadata.lock.9ONHM1?: Permission denied and still I cannot use gnome-software. I also get 2088879 – rpm-ostree update gets stuck when using rpm-ostree by terminal.
So, basically, I cannot update. No way. 
