Perry Heinrich
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I used McEdit to remove the chunks that were generated with a different seed then set the seed in the server.properties file to the original seed. Everything looks ok so far. However, I would like to point out that I'm apparently not the only one with this problem. I see a discussion on the forums from back in mid-January with a similar problem: http://www.minecraftforum.net/topic/2259145-server-is-replacing-chunks/
I have been unable to replicate the issue. I found the seed in the original version, set that as the permanent seed and have had no more problems. That being said, I can't say for sure that the problem has gone away, I just don't know how to replicate it. Reading the previously mentioned forum thread, it looks like I'm not the only one who has had this problem though.