I do understand you are using your correct Apple ID at Settings > [name on top]. My point was that there are at least 5 locations as provided in my previous post where your old Apple ID could still be used, which is the reason for the prompt you are seeing in Settings. I'm not sure if you have reviewed those locations. The much forgotten about one is Game Center where it is very possible you could be signed into your old Apple ID there, while still using your current Apple ID that shows in the Settings page. At the bottom of the Game Center page, it gives you the option to Sign Out, if it is showing your old Apple ID.
The other instance of having an app on your phone from when you had your old Apple ID is possible. When you sign out of your Apple ID, it does not delete the apps that you had downloaded. They will stay there even if you sign back in using another Apple ID. If you were to try and update the old App it will ask for the old Apple ID password to continue. This is why your old Apple ID would still be attached to your device prompting the Update Apple ID in settings. In this case, removing the app would remove the need for the prompt to update your Apple ID in settings for your old Apple ID.
It is also not unusual to be using your main Apple ID and use a different one in the Media & Purchases section. Apple deleting your old Apple ID will not remove it from your device if it is in one of those locations. This would have to be done by you.