First off, Dio is never, and I mean never, taking SK’s soul.
Secondly, all this talk of erasure and killing SK in the time stop. He can change his fate even after he has died. Dio manages to kill SK? He comes back instantly and kills Dio.
Thirdly, there is so much other stuff SK has that keeps Dio from doing anything. Dio and TWOH can’t touch SK at any point or he just copies everything they have, this also happens if SK looks at either of them, any and all damage just makes SK stronger and tougher, said damage is reflected onto Dio, is passively intangible etc etc.
And on the Almighty negging time stop, time stop exists in Bleach so SK nulling it is definitely not a NLF especially since TWOH is Dio’s power. Almighty just makes it side with SK.