When you load a chunk which has blocks that do not exist in it they leave holes in the world and do not cause block light updates. This appears to be vanilla lighting behavior and has been tested in Phosphor and Starlight. The best way to reproduce this is to add a mod to your game that adds blocks, place them down exit the game remove the mod and reload. When you rejoin they will be removed from the world since the registry entry for them does not exist. The blocks that were removed appear they have no block light because they don't cause lighting updates when they are removed.

These blocks aren't set to air in the traditional manner. There's no hook for me to insert into to even detect it.

This kind of breakage is expected for loading worlds that had mod specific blocks without said mods installed.