Runa remembered everything. She recalled how they switched bodies the second time and how she was killed by her half-sister, likely for the purpose of switching back to their original bodies.
Even though Yohana might have initiated the switching for her own gain, Runa ended up reaping the harvest in her stead. Yohana must not know the law of the switch, which would return the time to when they first met each other.
So when Runa heard the news of Yohana's capture, she ordered a maid to release her. If they did not meet at that time, they wouldn't switch back to this particular time, and anything that happened afterward wouldn't be rewound.
The other reason to release Yohana was to prevent her from meeting with Niels because she was afraid that they would fall in love with each other all over again.
The second switch proved that as long as Yohana was around Niels, Runa would never get the chance to win his heart.
