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It sounds like Proton VPN (or its repo) is causing issues for you. Given that it's a paid service, you can probably contact their support.
Alternatively, you can also look for the repo file in /etc/yum.repos.d, something like /etc/yum.repos.d/file_name.repo, for Proton VPN. You can then disable it by renaming it to .repo.disabled and try again (sudo dnf upgrade in the terminal). Note: This is not really a permanent solution, as it will disable updates for Proton VPN.
A lot of times you will see the format string for the fedora version in the .repo file. This means its probably looking for f41. Since fedora updates fast, third party repos are usually slow to move to the next version and this repo probably doesnt exist causing dnf to fail. You can try and change the format string to the last available version. It usually works without issue, and updates aren't disabled as long as the vendor updates that version
You should also be able to disable the repo from within the Software store app
did you download & try to install it or is it coming from your package manager?
I had something similar going on in Fedora Silverblue. I didn't really want to fiddle with it at the moment, so I just uninstalled whatever I got from ProtonVPN and the update went smooth afterwards. I hope someone else can point you towards a better answer.
I'm pretty sure just using the "sudo dnf update --refresh" command in terminal will fix this problem. It will ask you verify those packages new repositories. After that, you should be good using the store again for updates. This is assuming you upgraded from Fedora 40 before these errors occurred.