I have a theory that I hope answers at least one of the many retcons spotted in Silent Hill: Revelation. As it's a theory, it should be taken with a grain of salt, but I will use symbolism to help explain.
Between the two films, Rose found half of the Seal of Metatron and used it to send Sharon back to Christopher in the real world. Rose mentions to him that the other part is still missing, so the seal is not whole.
This is where my theory comes in.
We can infer from the end of the first movie that Sharon and Dark Alessa recombined after locking eyes during Alessa's "final" revenge.
Seeing, though, as Rose only had one part of the Seal, I theorize that, when she sent Sharon back to the real world and Sharon lost her memories of everything that had happened in the first film, Rose may have also separated Dark Alessa from Sharon. This is where the "two halves of a whole" comes in. The half of the Seal that Rose used can represent Sharon, while the missing half (inside Leonard Wolf) can represent Alessa. Since the two halves of the Seal were separated, then symbolically, so were Sharon and Alessa once more. While this may not be possible, it may also not be impossible either. Remember: grain of salt.
No, I think its a decent theory and a plausible one at that. Of course, we could be trying to make sense out of a movie that didn't make sense, but at least it's better than the alternative: Bassett just butchered the movie.
I know a lot of fans of the games hate the first movie, but it's a good movie. People have to remember that they can't follow a video game to the T or there would be so much useless crap in it. The story was plausible, and it had the creepiness that was perfect for Silent Hill.
Because of that though, it made no sense to have this movie follow the plot of the 3rd game. So, having this theory helps to bridge the gap between the two movies.
Alessa is a basically all-powerful creature that knows everything that happens in her world. If the cult knew what the Seal was capable of (and they obviously did), so did she. There is no way she would have ever let Rose get the seal, and it's even less logical that she would then let Rose use it on her. Dark Alessa states that she intentionally sent Sharon out into the world, making no mention of a split caused against her will. It's a retcon.