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.