I think a big clue that hasn't been discussed much is the fact that for now, he can only remember the first part of their relationship. I have a couple ideas of why this could happen.
1. Although I wasn't a fan of the "Navani is his wife now" theory, I think this is a good indicator it might be correct. As his relationship with Navani progresses, his memories of Evi will fill in.
2. Maybe for whatever reasons; his love life, his world-saving responsabilities, his Nahel bond, etc. he will no longer be pained by the earlier memories of Evi. When more memories won't pain him anymore, they'll return.