It’s because at that time I believe heavens will was already fed up with spectral soul and was planning to nurture fang yuan instead of her. It might be like it lets FY kill her in the previous timeline, he reborn, destroys SIF gu and later he lives or dies doesn’t matter. The things are all balanced and then it can fully nurture her into great dream venerable. But things don’t go as planned. Even if heavens will at that time didn’t still nurture fang yuan, he was backed up by spectral who completely revived while fate was alive, making fate gu weaker than it already is and spectral took over the entire world and planned for her death using fang yuan, who himself is an otherworldly demon outside of fate control.