One was too many. Why not just downplay or ignore elements that you don't care to focus on instead of twisting yourself up in knots over it?
Here is a great example. Say you are a writer who hates Krypto and doesn't want him anywhere near Superman. Just don't mention Krypto then. You don't have to retroactively remove him from continuity through complex space time weirdness to get there.
That way when a day comes when a new writer DOES want to use Krypto in a story they won't have to do even more complex BS to get him back.
You can pretty much use that example for anything Superman related. Don't like the idea of say Superman operating as Superboy in Smallville for a time? Don't mention it in your story. Every time they try and take stuff away from the Superman mythos it leaves it a bit poorer. Leave EVERYTHING intact for future writers to play with.
Superman is approaching Hawkman like levels of weirdness with all of his many origins and reboots at this point.
Superman has a wonderful and fairly simple origin. But it's what happens after he becomes Superman on Earth that the story really begins. Let's just focus on that ok DC?