So when you did the ls line, that listed files. Inside those files are lists of repo URLs, and that’s what I meant by ‘line’. It’s highly unlikely you deleted anything important as both those files looked to be full duplicates, but make sure to be careful.
The only line causing trouble now should be https://apt.packages.shiftkey.dev/ubuntu any InRelease. Your system is likely fully updated except for any updates for software coming from that repo. If you want to be certain, find the line with that URL and temporarily put a # in front of it (remember to remove the # when finished). This will disable the repo and allow the system to update without error. But for your system to update software from that repo, you’ll have to figure out what happened to the certificate.