Emerich, where do the stamps reside and from within the files you are using / linking, do the files point at the same Zone Stamp?
Editing the Zones (700 in one file or 350 in two files, etc.) would be best done in a 3D view (are you trying to edit them here?) where you can see and select as many at a time as possible. If it's not possible to edit all in one go, then selecting groupings of them across stories in the 3D window might help.
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