i had a hard time finding any info regarding Le Bel Homme (aka Utsukushii hito) on this forum. but here's my explanation of the ending.
towards the end, the story becomes a big psychological mess. it first started when miyuki temporarily loses her memory, then later regains it - both initiated by great trauma caused by the clicking of the gun. i think the term "regression" can be applied here (freud's defense mechanism in which one moves back in time to a period of safety and security).
in the very end when misaki calls miyuki by his late wife's name (yoshiko), imo he also undergoes retrograde amnesia (lack of memory regarding events that happen before a traumatic experience). the clicking of the gun was the traumatic experience for him - when they were on top of the hospital roof. it "triggered" this type of unconscious motivated forgetting. it was the culmination of events, especially after misaki learns after all this time he was wrong about his wife - yoshiko was not unfaithful but indeed loved him, only that she was forced into the position that ultimately labeled her as promiscuous.
subsequently, misaki can also be described as undergoing some sort of regression. miyuki, on the other hand, accepts her position as yoshiko's replacement after considering everything misaki did to save her. nevertheless she did say that she was "the mint", emitting a sweet fragrance even if turned into a herb. the sweet fragrance in this case is her face, a replica of yoshiko. in a way she is also turned into a herb, losing her own identity to fill the void of another.
(to what extent can all this be true? possibly close to 0. retrograde amnesia results from damage to certain areas of the brain and as far as i know, cannot be reversed. also regression usually refers to going back to a time of safety, as in childhood)