Yes and no. I can now remove the “Use same boards as this map” map.
However, the fix has unmasked a further problem, one that I have seen before when trying to change the name of a board. That problem is that, after removing the association to another map, the map just displays its background colour. Nothing more, no board image and no At-Start Stack (unless, I found, associated to “[Any]” board rather than a named board, but then I still could not get the board to display its image).
Initially, I was using the same name for the board across several maps. I don’t think this should be a problem, but just in case, I changed the board names to make them map-specific. This made no difference - and I did amend the At-Start stacks to point them to the new board name.
In summary, the change in VASSAL-3.6.4-SNAPSHOT-dac8765-master does appear to have worked but it will not be useful whilst this further problem exists.
As a workaround to both problems, I completely removed the corrupted maps and re-built their definitions. It helps that I was able to copy in and edit definitions from the “master” map.