I think its because during the historical time which is their first timeline there is a blue colored flower gem that they cherish since it symbolises their feeling with each other and from what I remember Kihoon carried that when he was sent to a war to remember Yeon. And since kihoon remember their past life he also got yeon the same colored blue flowers to yeon before the flashback happen. So I think since now that Kihoon doesn't remember a thing he got Yeon the most common colored of rose which is red. (Sorry for the confusing explanation)

I can't remember the significance of blue vs reds roses?