We don’t have a custom runtime version, but what you describe is the exact same thing that happened to me (EAS Updates not appearing due to 'Failed to download manifest from URL' error)
At first the update worked, then I did eas update again, and now the app won’t get any of the updates at all, and has fallen back to the app store version (I guess because of the error I mention in my thread) but I have no idea what’s causing it. This is a major problem.