DH generates the wrong chunks.
You can see the difference in the image. This is on an older server map where all of these chunks have already been generated. So DH should be reading the chunk block data already present, right? But instead it thinks these are empty chunks and it's using new (modded terrain) world generation to make the LODs.

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When I physically fly over the already generated, old server map chunks DH will correct how the LODs look, but this map is 10,000 x 10,000 blocks large and I would prefer not having to do that...
How was the map created?
Many third party programs output corrupted and unfinished chunks
Vanilla MC has good error correction, but DH requires the chunks to be as they are suppose to
Try optimising the world (vanilla feature) that should update the chunks format
You can also in DH settings, enable recalculate height map and assume existing chunks are finished
Hmm. I was thinking this may be why. I used MCA Selector to import the map and merge it with another map of mine. I'll try your suggestions though.
Ayy this fixed it. Thank you so much!