It’s Motion Blur issue. Namely, Motion Blur applied to shape layers of nested comp with animated Scale.
Due to the big time skip at the problem point, Motion Blur acts weirdly, sampling frames far from actual frame.
The “disappearing” elements are elements with applied Motion Blur that samples frames from time where Scale=0%.
By default Scale animations are rendered before Time Remap. Collapse Transformations makes them being rendered after Time Remap.
Another fix is to set Shutter Phase = 0 in nested comp settings (Advanced tab).