The song actually started with a different title and completely different lyrics. When Lloyd-Webber began his relationship with Sarah Brightman he wrote a song for her titled “Married Man” with lyrics by Trevor Nunn. He later decided to rework it into Phantom. Phantom itself went through three lyricists. After his first choice turned him down...
Alan Jay Lerner was then recruited, but died soon after beginning the project, and none of his contributions remained in the show. Richard Stilgoe, who also wrote the lyrics for Andrew Lloyd Webber's Starlight Express, then wrote lyrics for the production, as well as devising most of the titles for the songs. However, the composer felt that Stilgoe's lyrics were too witty and clever, rather than romantic. Charles Hart, a young and relatively unknown lyricist was invited to rewrite the lyrics, even contributing almost solely to an unplaced tune by Lloyd Webber, which later became "Think of Me". Some of Stilgoe's original contributions are still present in the final version. From Phantompedia
This shows Lloyd-Webber’s notorious perfectionism. He is certainly not averse to making revisions after a show is already in production. After his most recent show, the sequel to Phantom called “Love Never Dies” received poor reviews he decided to pull it off its West End production for several days to completely rework it.
As to the reasons why he made specific changes it would only be speculation. They may have been taken from earlier revisions of the show before Hart was brought in. He may have simply been unhappy with the lines and simply rewrote them. He may have been asked by a certain director or record producer to alter them. There’s really no way of knowing for sure.