It says in the Unending Journey when you look at the quest 'Our Closure'. At the bottom, after the part about Sid's reply, it reads this:

'Time to go. I don't know when we'll do this again-[I]if[I] we'll do this again. The little trick you've learned doesn't count, you know. But even if this is our end, it won't change what we had. I love you more than you'll ever know. Be well.'

I'm not sure what to make of it entirely, I'm batting in the dark with this one, but I think this is Fray accepting that the WoL's Darkside has been embraced in a way, and not in the way they originally thought back in Heavensward. But to them, that's OK, because they have come to terms with being you and who you are, you and your Darkside truly fight as one and Fray will love you for it no matter what, because ultimately, this is who you are and you finally are completely at terms with that. The flower was in memory of who you and Fray used to be, a tribute to your start as a Dark Knight. It is a rather sweet way to end to this aspect of being a Dark Knight, you and your Darkside see the world through the same eyes and even though the odds of you seeing each other again are slim, you know that whatever happens, you both have each other and like family, you'll love each other to the bitter end.