possibly make it so you can export wld to xml and assign each part of the zone geometry a node-id... then put your changes in an xml file of the same format, and when you want to patch the normal wld to a new one, just load up the xml and it'll say 'ok, this node is different' and patch it.
of course, this is very rough, and i'm incredibly tired while writing this... so it's entirely possible that this isn't possible... but it's an idea nonetheless...
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