While this may or may not be a full answer, I wanted give some basis, especially since this is a wonderful yet unappreciated system:
Any of the "create thing such that it always existed" or "remove thing from ever existing" effects in anima represent extremely powerful forces not commonly available to nearly anyone. I won't bank my reputation on this to say "all", but nearly all the effects for that you see come from High/Divine Magic, High Gnosis Entities, or artifacts that run off of one of those two things.
Reality is a malleable thing in Anima, just not an easily malleable thing. Gnosis isn't just how much fate seems to like you, after a certain point it's an measure of how much ability you have to nudge reality to your wants (which is why Gnosis 40/45 entities are usually exempt from a lot of effects caused by anyone not on their level : their reality-pushing status has gotten to the point where they push back on the world so much that they can no-sell anyone else's attempts to push on them)
The powers your mentioned are the rare things that are by design meant to restructure the world. And by design, the world contorts and distorts to accommodate. For most people, you are included in that mechanism of reality restructuring. Your memories and life twisted to fit things too. So by the current rules of the world, all your memories are "100% real", and you'd never know the difference unless you're high enough Gnosis entity to no-sell the change on yourself, or tap into an artifact or magical power whose nature is to see beyond the current revision of reality (if there can be powers to change reality, it of course makes sense that some powers tap the same mechanism to give 'read-only' access to reality's revision tree).
How/if these higher beings see meta-reality is a complicated question, but it's assumed that they do see the world different than we do, which is why the Beryls and Shajads have immense but still imperfect foresight on the fate of major players in the world.
Time travel/viewing dealt with more specifically usually is stated to have the above caveats in mind:
1) High Light Magic spell Predict :
Of course, these predictions are not infallible; what is seen is only
the most probable destiny, which may be changed through the
intervention of higher powers or the actions of persons with elevated
2) Divine Destruction Magic Uncreation :
No one who knew of what was unmade remembers it, and all events it may
have affected are modified as though what was unmade had no part in
it; even returning to life those whose death the unmade might have
caused (as long as their souls were not destroyed). Only entities with
a Gnosis of more than 40 will be conscious of what happened.
3) Undo Time :
This spell makes the flow of time run backward, rewinding any event
that has occurred within a period determined by the level of the
spell. Thus, the caster can repeat a few turns or even restore life
to someone who died in that period of time. Only the caster, beings
with Natura +15 or greater, or divine creatures will remain aware of
what happened in the rewound period; for the rest, those moments never
passed. This spell cannot undo actions in which a being with Gnosis 40
or more was directly involved, unless the caster has an even higher
Gnosis, nor return to life a soul that has been destroyed or
desecrated. It is important to point out that time in general does not
flow backwards, but rather the spell separates out a small
part of the space-time continuum and makes it rewind briefly.
This way, the short temporal distortion is less harmful to the flow
4) Note about time-magic in general :
Unlike other Paths of magic, all time-related spells in Gaïa
are severely restricted and controlled by the Powers in the
Shadow. Therefore, any spell that might possibly cause real
alterations in history or disruptions to the space-time continuum
will be overridden by systems of Imperium and have no effect.
As an personal interpretation : I don't think Imperium itself has Gnosis 40/45 ind
In these and other examples theres a strong note about destruction still often being irreversible : if someone's soul was destroyed it's irreplaceable. You can change reality all you want but you can't recreate what you've lost the blueprint for.
In conclusion: reality itself changes permanently, and most time magic can't see through it since reality was changed in complete past/present/future. Because this is exactly as dangerous as it sounds, access to reality warping is very restricted.
Your assumption about time viewing seeing otherwise is incorrect (most of the time, with the exceptions I mentioned), is the quickest way to explain it. Only high Gnosis entities or similarly powered effects will ever know something changed.