The first change is near the beginning/middle  where Okabe is going back to the lab to time leap back from 8/15 to 8/11(I don't remember when exactly this happens, it might even be back during episode 19's events, but I didn't realize it was missing until episode 20 since I didn't remember when exactly it happens). As he approaches the apartment he sees that machine is in mid-activation, and when he gets there to check it out, the lab is empty.

This is already a huge loss because this moment really got you wondering right from the beginning. "Oh crap, someone else is time traveling, who the hell is it" and it's on your mind throughout the whole chapter and made it a more enjoyable experience.

After that, there's no major change until they discover Braun getting the IBN. While I'm at it, I'll just go into detail.

First, they go into his house(Kurisu waits outside, doesn't come in with them). Also, shortly after he reveals himself as FB, he draws his gun and has it pointed at them for the entire conversation, added to the suspense. The anime kind of changed this to just a casual 'sitting down and talking' atmosphere that I thought was kind of disappointing(also, they have this conversation still in the house)

The conversation itself is basically the same. At the end, he changed the direction of the gun from Moeko to his own head and blows his brains out, he doesn't kill Moeko in the VN(in fact, he's made out in the VN to be protecting Moeko in his own way, which is why he stopped sending orders. Rounders are killed after their mission is over, so he basically wanted to try to stall her mission out for as long as possible. Following that logic, he would never actually kill Moeko himself. Of course, he acts like a villain on purpose and this is just a conclusion that Okabe reaches personally after adding up all of his actions, it's not 'confirmed' as truth, just what Okabe thinks.)

So after this, he checks Nae's room, since this all happened when she was in the other room sleeping, only to find that she wasn't there. Anyway, at this point, they all decide to head back to Moeko's apartment for the time being, after which Kurisu mentions that she saw Nae run from the house shortly after she heard a gunshot.

Moments later, there's a knock on the door. Knowing of Moeko's fate to die today, Okabe has a bad feeling and tries to stop her, but is too late. She opens the door and at the door is... Nae. She immediately stabs and kills Moeko. She proclaims that she'll kill Okabe in 15 years and to wait for her in fear(I would also like to point out that Okabe's year of death in the SERN timeline was established by Suzaha in the VN prior to this point, 2025.) and takes her leave. Kurisu and Okabe just stand in stunned silence, after which Kurisu suggests that they hurry up and undo the d-mail and change events. You can do that now and skip what comes next(basically jumps to the same point that this episode ends at), or hold off and see the optional event, since Okabe thought that Nae was acting like a completely different person and Okabe wanted to get to the bottom of things.

Doing so makes him time leap back to those events, time time he sends Moeko in alone, upon hearing the gunshot, he sees Nae run out and chases after her.

Upon speaking to her, he basically learns that she found out later that Moeko and Okabe were the ones in the house the day her dad died, and blames them for the death. Her hatred basically grows over the years while she waits until she gets old enough to exact her revenge. She captures Okabe and tortures him to death 15 years later, but then learns that Moeko already died years ago, and was not able to exact her revenge upon her. So, eventually she gets her hand on the time leap machine that they created, which is kept by SERN in storage somewhere, and uses it to time leap back to that day, essentially jumping 15 years in 48 hour increments, which means she time leaped thousands of times in succession, all to fulfill her revenge(and you also figure out at this point that the person you saw using the time leap machine earlier was Nae, finishing up the last of her thousands of leaps). So the Nae you see at this point is one that already tortured and killed Okabe to death in the future, which of course, she describes to Okabe(needless to say, hearing all this stuff come from the mouth of a little girl is creepy... and maybe kind of hot, ahem.)

Basically, she gives him one good stab for the road and runs off, and at this point, Kurisu catches up to him, worried about his injury, he tells her to send the d-mail now, she complies, knowing that it'll get rid of his injury, and then we're back to the end episode 20 again, of course with some additions to his inner monologue, with Okabe remarking that now Nae's revenge won't happen in this worldline.

And that is what was cut out!