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A zip archive can be overwritten when you call Save().
It won't have anything to do with whether you add folders with subfolders.
Suppose you instantiate a ZipFile with a filesystem file, like this:
var zip = new ZipFile("myarchive.zip");
...or, like this:
var zip = ZipFile.Read("myarchive.zip");
If you later call zip.Save(), the original zip archive will be overwritten, with whatever is in the instance.