Saw this comment somewhere else, and I think it makes perfect sense actually
(from someone’s comment in CN community and roughly translated):
Phrolova said that the violin was the most perfect gemstone, a gift from the entire village to Phrolova. However, she could not find the violin, so she had to use a gemstone imbued with the power of Leviathan as a substitute.As rover prepared to pick up the violin from the water in Lost Beyond, she was pulled into the depths of the sea. After being stabbed through the chest by rover and falling off the platform, Phrolova also plunged into the depths of the sea, where she finally discovered the violin. By then, she no longer needed the gem's power.Phrolova picked up the violin and began to play. When the people around her appeared, she had finally completed the performance of this piece (she had always wanted to incorporate the villagers' complete frequencies into it)
The “I'm sorry” Phrolova uttered was actually directed at rover. When she fell into the depths of the sea, she finally realized that without rover, she might never have found the violin, and certainly would not have been able to complete her composition. As for why the violin could replace the gemstone, Phrolova explained that to transform Lost Beyond into this world, a clear “weave” was necessary. However, she had been misled by the Fractsidus into believing that the ‘weave’ was the gemstone, never realizing that the true “weave” was the violin itself. The energy sea where Phrolova ultimately fell was the energy sea beneath the “Lumen Tower” on the map. Perhaps the energy here could rival that of Leviathan within the gemstone. When we returned there and looked down again, we will find a thick fog.
Therefore, after Phrolova fell, rover could not see what happened to Phrolova below. Rover’s closed eyes may have been a sign of mourning, or perhaps fickle (not sure if this is right term), but more likely, they were a sign of uncertainty. However, compared to confirming Phrolova's situation, the unresolved mystery of Fenrico was more important, so he had no time to consider Phrolova. After speaking with Fenrico, rover once again saw the petals of the red spider lily, his eyes filled with surprise. This made him realize that Phrolova was not yet dead, so he told Abby that there was an important matter to attend to. In truth, this important matter was—keeping the appointment (the one rover promised to attend). At this moment, Phrolova's melody had been completed through the “violin” (weave), and rover also needed to fulfill his promise (“When this piece of music is truly complete, I will definitely return.”) Thus, after the chapter ends, rover can enter the Lost Beyond on his own.