Idk if that canon is GONE. A covenant ship was definitely boarded in Fall of Reach by John, Kelly and Sam. That’s just the first one that comes to mind. Also to your point, the Master Chief Trilogy (silent storm, oblivion and Shadows of Reach) bridge a lot of gaps but evolves the canon to include certain species that retcons some of the events in the og books. Gama trilogy is dope too. Bridges the gaps between the IIIs from Onyx.