If you use the /fill command to change water into lava, it changes it mostly to obsidian
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For now I'm not going to change this behavior because it would cause a performance hit for ALL fill operations. For this special case I recommend a workaround by filling with another block (like stone) first and then with lava.
Fixed in 1.9.3-pre1. However a related bug seems to have appeared, see MC-101298.
Can confirm. Work-around would be to replace the water with an arbitrary block first, and then replace that block with lava.