I would second the suggestions of just inspecting your particles (maybe in the context of denoised mics where contrast is higher) and using mass photometry to compare the mol weight in the presence and absence of substrate.
Also - this may be a case where non-point group symmetry expansion and local refinement, as described here and here, may help to significantly improve resolution and help resolve the intersubunit interfaces.
Separately, you might want to try local refinement around the two ends of the whirl - say the last three or four subunits masked together - and see if that helps clear up what is going on at the broken interface.