As best as I can tell, this is resolved by changing the lines that actually plot to:
meshscatter!(ax, bodies, markersize=0.1, color=clrs, clip_planes = Plane3f[])
linesegments!(ax, lines_vec, color=clrs[1:length(lines_vec)], clip_planes = Plane3f[])
Don’t know many details, picked this up when trying to figure out a similar issue and found this: Clipping defaults changed when upgrading to GLMakie v0.11 [noticed in Brillouin.jl] · Issue #4741 · MakieOrg/Makie.jl · GitHub
Edit: It is in the documented attributes for e.g., meshscatter:
clip_planes = automatic — Clip planes offer a way to do clipping in 3D space. You can set a Vector of up to 8 Plane3f planes here, behind which plots will be clipped (i.e. become invisible). By default clip planes
are inherited from the parent plot or scene. You can remove parent clip_planes by passing Plane3f[]