That even if your are explicitly told that your memories were rewritten by Omnipotence, the effects of Omnipotence remove that knowledge and understanding until it no longer bothers you and you forget all knowledge of Omnipotence.
In the most recent chapter of Boruto, he tells Shikamaru that he’s heard the effects of Omnipotence multiple times; but that knowledge was removed gradually until he only had his own rewritten memories and therefore forgot all knowledge about the technique and forgot even discussing it. And Boruto states that Shikamaru will forget that conversation again.
Sasuke mentions in the last chapter of Part 1 that he knows something isn’t right due to many factors, such as Boruto having Momoshiki’s soul residing inside of him when he should be in Kawaki, and Boruto having his old headband when he remembers giving it to Kawaki. But that despite those inconsistencies, he can feel that wonder and unease slowly vanishing and becoming more comfortable with the idea that Kawaki is Naruto’s son, not Boruto. This was due to Omnipotence.
It’ll remove those doubts and inconsistencies and the knowledge of Omnipotence until the will of the caster becomes absolute.
The only person who seems to be grasping the concept of their memories being altered is Amado. Because he recognizes his own work on the scientific tools used to modify Kawaki’s body being inside of Kawaki and not Boruto, as well as Kawaki having his daughter’s genetic makeup in his restored Karma while Boruto still has an original. And states that it’s a form of signature to recognize his own work. This leads him to deduce that his memories must’ve been rewritten, but he doesn’t explicitly know that it’s due to Omnipotence.