ChimeraX (and Chimera for that matter) connect atoms in standard residues using a connectivity template.  Therefore the atoms have to have standard names.  Some hydrogens in your file don’t have their PDB-standard names, and therefore wind up unconnected.  I have committed a fix for this — if there are unconnected hydrogens after the template pass then Chimera(X) does an additional connect-by-distance pass.

A second problem with the file is that it uses ATOM records for everything, including solvent, ions, and the lipid bilayer.  ATOM records are for polymeric residues and imply connectivity between consecutive residues with the same chain ID.  Therefore the non polymeric components of the file should have been using HETATM records.  I have attached an edited version of your file with appropriate HETATM records.  It should work much better in tomorrow’s fixed build.

—Eric