VLM is static and exist in persistent level, it doesn’t get streamed with sublevels. You should always check how VLM grid is positioned relative to level’s geometry, ideally all samples must be in empty or solid spaces, border cases may cause issues. Default grid size of 200 is mostly too much for small levels (indoor scenarios) so you should diminish it, also having grid too sparse gonna cause lights to bleed through walls due to interpolation. At the same time having it too dense would put the stress on VRAM as VLMs are preloaded there.
Pitch black probes may be the result of them being under the landscape (even if lanscape component is hidden or made invisible by ‘visibility’ tool) - there is the setting to disable this “optimization” in project config. Also if you use sublevels they may be loaded into Lightmass all at once causing incorrect shadows from ‘nonexistant’ objects.