I'm not sure why coordinates get offset during the transition from s3d-based (WLD) to eqg-based (ZON/TER). I'm pretty sure I made it write the raw vertex coords from the s3d to the eqg, and as far as I've been able to tell there are no global offset values in the WLD data (maybe hardcoded... or I missed something somewhere). You can set global coordinate offsets for the eqg-based result in the tool (the models or objects tab (whatever I called it) has an entry for the "all the geometry in the zone" model and you can set its "position" there), but trial and error would be pretty tedious for that.
Zonelines work differently in eqg-based zones, iirc they are cubic areas you can specify in the "regions" tab. Not sure how they line up to what the client sends to the server, though... Probably easier to use scripted zonelines. I never tried transcribing the zoneline data from the s3d-based source or anything like that, because WLD format sucks.
I'm surprised you even managed to edit a zone, the mass of geometry was pretty intimidating whenver I opened one up in Blender myself ;p I figured it would be easier to make something from scratch following a tutorial or something and getting textures from the web.
I thought there already was an old tool for working with s3d-based zones without converting them to eqg, which might be what you'd want instead. I couldn't be bothered to learn about generating BSP trees and breaking the geometry down into little logical regions based on that like s3d-based zones require... eqg formats are much more straightforward.
Other than that... there's not a lot of interest in this stuff in general, I don't think. Too much work.
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