@warpavp2: I haven't tried just copying over region, but I highly doubt it would work going from A16.4 to A17. You'd probably be best to use creative menu, spawn in the stuff you need, and start from scratch.
As far as copying over the same seed: Let the server build the new map using your seed name, then shutdown the server, copy your old game files back.. might work, unless you're trying to go from A16.4 map to A17.
Also: I suggest you do NOT use the default serverconfig.xml filename as is.. change it to something else, such as serverconfigWarpavp2.xml... because every update re-writes the default serverconfig.xml file.