Semilla @viki translated some of the scenes that were either cut out or not filmed at all.
For example this is the ending that they changed last minute:
100 years before CY's time, but the same place under the tree. ES with a straw hat and a staff walks to the place where CY was lying. She drops to the ground and starts digging with a stick. Next to her is the aspirin bottle full of yellow mums. ES puts the aspirin bottle inside the hole and covers it with dirt, as if to plant the bottle.
ES's narration: That is why I go to the heaven's door every day. I believe that my faith, rather than my calculations, will bring me back to him. Believing is the easiest thing to do for me now.
The bunch of yellow mums from ES's aspirin bottle look as if they grew there. (No other yellow mums should be around in the area)
[More description of ES going in and out of the portal. She observes which flowers are around to check whether she's coming back to the same time or not. Then follows the ending we saw - ES going to 4 years after her departure. There is indication that for her, it took about a year to finally make it to this time.]
ES approaches the tree, and the whole area is full of yellow mums. However, there is nobody under the tree. She gets closer, then turns around, and CY is watching her with disbelief in his eyes. ES takes off her straw hat. CY stares at her, speechless. As if to shake off an illusion, he looks away, then looks back. As if he's whispering, "Imja…?" Like that, they stare at each other.
[Description of the beginning of episode one when CY and his men in cloaks were escorting the king and the queen from Yuan to Goryeo. Ends with CY looking up the sky.]
[Back to the place under the tree when ES left.]
CY is on the ground, eyes closed, looking dead.
One by one, rain drops start to fall.
ES's voice: I like the moment when rain starts to fall. One by one, when the rain drops land on my forehead, "Huh?" it makes me look up like this.
CY's one arm is extended onto the yellow mums. He opens his eyes and turns his head. His hand touches something among the mums. He moves the yellow mums aside and find the half-uncovered aspirin bottle. He grabs it, pulls it out. Meanwhile, his heartbeat can be heard. At first, it's a soft and slow beat, but gets faster. He manages to look at the bottle closer. It's really old and dirty with moss, but it certainly is an aspirin bottle. CY gets his own aspirin bottle out and holds the two of them together. The heartbeat sounds normal now.
Under the pouring rain, CY starts to smile. He'll live.
[Back to the ending scene]
ES walks toward CY. Then she starts running. CY opens his arms wide. He's overcome by this unbelievable miracle. ES dives into his arms. CY embraces her.
Personally, I do think the writer's version is a bit cheesier and less CY-like. But still, they could have hugged!
Also, the message from ES that says "It's ok" was in the scene where Gi Cheol and his people were hiding. CY recognizes the letters from back when ES did the Love Actually thing. He surely does remember everything about ES!
In conclusion, the writer added the aspirin bottle as another clue for CY to trust and wait for ES, but the director chose to just have ES's words from the previous episode- "I don't think I'll be ok. Even if I went back, I'll try to come back to you, and the portal may take me to other worlds instead, and I'll wander aimlessly until I find you" (something like that... not exact quote because I'm too lazy to look that up).- be the only clue for CY to have hope. I guess that makes it more dramatic.
I really like this ending so much better. The idea with the aspirin bottle is really neat and also I would loved to have heard Choi Young say "Imja" one last time....
You can check out the full thread on the deleted scenes here