It makes the most sense for Eun Byul is alive!
It doesn't make sense that someone good at swimming will drown, especially after we know that she DID pull out Eun Bi out of the water. Of course the mystery of WHY the police decided that the corpse they found is Eun Bi (there must of found something to think that) is one of the KEYs to solving the mystery.
Another thing we need to find out is WHO is behind this text messages and pranks. As Eun Byul isn't the only one receiving them that means that there was an accident (maybe bullying) that all this people are involved in that led to Soo In to commit suicide. Now someone is taking revenge to the people they think is responsible for Soo In's death - its either her mother or someone she was close to. Soo In's mother clearly knows something as you can see the scary look in her eyes and her sinister smile, she may be well aware that Eun Byul right now is actually Eun Bi.* This reminds me of 'White Christmas' - where a few students got anonymous notes and they had to solve who was behind it... (I won't give away what happened as its a really good drama to watch, and if you have watched it already you will know what I mean).
Ah, and it doesn't make sense for the SHADOW person (that's how I call the person behind all of this) will actually kidnap or kill Eun Byul - simply because judging from his behaviour he wants her to suffer, and if she dies its over. That means that maybe with the whole accident (Eun Bi trying to kill herself and Eun Byul disappearing) Eun Byul found the perfect option : to exchange with her sister (this giving Eun Bi the chance to live the life that was stolen from her, to have a mom) and it gives Eun Byul the chance to be in the shadows and try to find out who is behind the messages and pranks.
It is the theory that makes perfect sense, more than the chance of her drowning.