To say that Spiritual Realm is "all places and all times" or that time and space do not exist there is a bit misleading.
They're not nearly as important as in Physical or Cognitive Realm, but they are in Spiritual too: for example there are Connections to places (which would not make sense if all places were one in Spiritual) and we know that Spiritwebs degrade after death (which again would not make sense if time did not exist in Spiritual).
For example, you can look into past and future because time exists in Spiritual Realm. It's just it's not as binding, it's just another dimension in there, like height or depth in Physical. Just like you can look up and down, you can look into past and the future in Spiritual Realm.
Does that make sense?
Following from that, when Nightblood consumes Investiture, it does not erase it from history or anything. It just vaporizes.