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The reported warning was being produced when writing the "end of central
directory record", in ZipFile.close().
Based on a little experiment with 70k test text files, the default
archiver in OS X appears to just use the number of files mod 64k in the
end of central directory record. I tweaked the ZipFile close() method to
do this, and the resulting ZIP file appears to work just fine, both with
the OS X archiver and with ZipFile (without ZIP64 enabled). 
There's a blurb in the ZIP format description about this sort of thing:
"If an archive is in ZIP64 format and the value in this field is 0xFFFF,
the size will be in the corresponding 8 byte zip64 end of central
directory field." I don't know if that means "the right thing" is to
switch the archive to ZIP64 format if more than 64k files are added, though.
If I have time I'll go look at some other open source ZIP
implementations, but I won't swear I'll ever get around to it. :)