I don’t think that’s the problem, and I wouldn’t really anything related to sources.list or anything in sources.list.d/.(*)
It does seem like an auto update thing, so got some quick suggestions.
Since you mentioned Discover, I’m guessing you’re on KDE Plasma, which is great because it’s what I use and know immediately where to go.
Go into the main settings and way at the bottom left after all the other sections, there should be a section labeled “Software Update”. The only thing you need to care about is the first option, which will be “Update software: Manually/Automatically”.
If “Automatically” is checked, try disabling it and then reboot. If that doesn’t, work, there’s a more useful GUI tool, but for some reason it doesn’t show up when searching the application menu (or at least doesn’t for me).
Quick command line thing here:
sudo software-properties-kde
This has a bunch of options which I won’t get into, but in the “Updates” tab, you’ll also see “Automatic updates” with a few more options than the one in Settings. I’d enable “Only notify about available updates” if everything else is enabled.
You can disable “Check for updates” entirely, but I wouldn’t recommend it. You can change that to “Weekly” or something, so that it isn’t constantly checking, but I don’t know if it starts up on every boot, so might be useless to change that specifically.
After rebooting, take a look at what the file /etc/apt/apt.conf.d/20auto-upgrades says.
It shouldn’t be too long, but depending on what the values might be for Download-Upgradable-Packages and Unattended-Upgrades, that could be the source of the problem.
Everything in that file should now have a value of “0” except for the first line (Update-Package-Lists which will have a value of “1”).
(*) Theoretically, your idea about sources lists could maybe be an issue, but I’m not sure. I don’t know if it’s possible that apt-get could be in some kind of loop if there’s a mismatch or duplicates with your repo sources. I’d assume it would error out, but maybe it’s just being weird.
For now, I’d leave that all alone. If none of the above works, I can give some instructions on dealing with third party repos, but I don’t want to make this comment any longer than it is already.