Dark Chunks after using Chunky

While setting up the world for a private server, I started with generating some DH chunks. I then figured, might as well use Chunky now since I will have to anyway, and hope that'll speed up DH generation afterwards.
After stopping generation with chunky, the new DH chunks seem to be dark.

Manually visiting the chunks doesn't seem to fix the lighting.

How can I fix the dark chunks, and/or avoid seeing them in the future? Is this a common issue with pre-generation of chunks?
Playing around with lighting settings doesn't seem to have helped with the existing chunks so far
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