Perhaps there are external factors at play. The world of demigods is full of chaos and danger. Reyna might be in a position where Percy feels he has to be by her side to protect her or to fulfill some greater prophecy that involves the two of them, and this leads to him leaving Annabeth.
Annabeth would probably be very hurt at first. She has a strong bond with Percy, and his leaving for someone else would be a huge blow to her self - esteem and her heart.
Well, it could be simply due to a different kind of chemistry. Sometimes in fanfiction, the author wants to explore an alternative relationship dynamic. Reyna has a certain allure and mystery about her that might attract Percy. And the story could be set up in such a way that Percy and Reyna have more shared experiences at a particular point in time, which makes him lean towards her instead of Annabeth.
One reason could be that she's scared. The idea of becoming a mother at that point in her life might be overwhelming, and she might think she can't handle it with Percy. Maybe she wants to protect Percy from the difficulties that come with the pregnancy as well.
One reason could be that Percy is still deeply in love with Annabeth. His loyalty to her is unwavering, so he might reject Reyna out of his commitment to his existing relationship. For example, in the original series, Percy's relationship with Annabeth is built on years of shared adventures and mutual understanding.
One possible reason could be that they grew apart over time. Maybe their different responsibilities in the demigod world led to a lack of communication and connection. Another reason could be external pressures, like the expectations of their respective families or the demigod community. It could also be that they had different ideas about how to raise their child, which caused irreconcilable differences.
Annabeth could be under some kind of magical influence. In the Percy Jackson universe, there are many magical elements. She could be cursed or charmed without her knowledge. This would be a very interesting take in a fanfiction as it would add an element of mystery and also give her a chance for redemption once the truth is discovered. Also, it could be that she has some internal insecurities that she hasn't dealt with and they manifest in this way, making her act out of character.
Well, one reason could be that in the fanfiction, the writer might want to explore a different dynamic. Maybe Annabeth gets lured by Luke's charm that has been newly developed in the fanfic. Luke could be presented as more understanding or having a different kind of allure that attracts Annabeth away from Percy.
One reason could be that Percy has shown great courage and strength, which Reyna respects. She might see in him the potential to be a great ally or even a leader. So, she becomes protective to ensure his safety and to keep him on their side.
It could also be a matter of self - discovery. Annabeth might have been on a journey to find out who she was outside of her relationship with Percy. Meeting this mortal was a turning point where she realized she wanted to explore a different path, even if it meant leaving Percy. Maybe she thought that being with a mortal would give her a chance to have a more ordinary life, at least for a while.
One great 'Percy Annabeth Reyna Fanfiction' is 'The Bonds Beyond Prophecy'. It beautifully explores the complex relationships between the three characters. The author does an amazing job of delving into their individual personalities and how they interact with each other in different situations, both in the context of their shared adventures and their personal growth.