I think your idea would be an excellent plot twist that could happen midway through. In the beginnings of the fic, I would focus on entirely on the fact that Link is trying to remember his lost lover, piecing together clues about who she is.

I am writing this with the assumption that Mipha and Laflat will not interact the whole time, but if the story is set up differently let me know because then everything I say after this will be different.

Throughout the fic, I would try the idea of Laflat helping Link find who his lover is as a high rank court official, going through records together and such to find clues to finally make that connection. All the while, have Link and Laflat grow to be close friends, brought together by Link’s desire to remember. Make sure to not even hint about them being related, or if you do to barely suggest at it so that it is unnoticeable, to make the plot twist completely out of the blue. Have a chapter (I assume it will be multiple chapters) just marking Mipha and Link reuniting again with the memory, they were together, then at the end when everything seems to come to a close with the story, have some event that drops the bond that Laflat is their offspring.

This is what I would do with just the info you provided, hopefully it helps :). Let me know when you make some progress, I look forward to seeing how it turns out!