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I've never had that happen, but I seem to remember it being caused by removing the base(default) terrain, usually sand or grass...depending on whether it's a lush or desert world. The key file could be a problem, too.
It sounds like the things you're deleting in
S3PE could be more safely removed in CAW after file conversion(sounds like you've already extracted). You do have to keep the base terrain, but should be able to change it to whatever you want in CAW, using Right Click > Edit on the base terrain paint layer.
It sounds like your mip maps haven't regenerated either, in which case the close-up view would be the accurate one.
I haven't extracted a world in like half a year, but used the info here, when I did...
http://www.modthesims.info/showthread.php?t=469942
Hope it helps