Been there, done that, broke it. I used Minecraft 1.0 to generate a world. ECC dates back to around April 2011, by that time (starting with Beta 1.3 in February 2011) the Alpha level format should have been replaced by the Region file format, which lasted until Minecraft 1.2 where it was replaced with the Anvil file format. I converted the Region file to an Anvil file, tested //setbiome a few times and restarted Spigot. And I guess we all know what happens when I test things. The control group (A world with the same seed, generated in 1.2) works fine. It is possible that the conversion from MCR to MCA breaks things. This is definitely not the result I wanted, but it happened anyway. Science!