Hi there, we've been having this problem for a while and have no idea as to why this is happening. For our level there are certain sections that feature grass, but whenever we try and paint the grass that was made from 'SpeedTree' everytime we bake there are deep black shadows running constantly through out it, even in a high noon, bright sunshine setting.
If anyone has any ideas please let me know!
p.s. for the lightmap resolution it was originally listed as '128' but we kept getting an error when baking saying the resolution was too high and was automatically reduced. We saw that the Lightmap Resolution had a arrow next to it to revert it, which we pressed and it set it to '4'. This also didn't help at all.
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If it does go away, then i'd check your UV2 lightmap unwrap and see if that is the problem.