I see two rational solutions of the issue (all written below is applicable only for allowZip64=True):

1) Always write Zip64 extended information extra field. This approach always successful, but the zipfile size will increase by 20 bytes for each file.

The first patch (zipfile_zip64_always.patch) uses this approach.

2) Write Zip64 extended information extra field only if assumed file size is more than a certain limit. In very rare cases this leads to the impossibility of compression of the file which can be compressed the first way. However it produces the same file as before patch in most cases.

The second patch (zipfile_zip64_try.patch) is based on Alan's patch and uses the second approach. The probability of errors is reduced and they are now detected and does not lead to a silent data damage.

Both patches are for Python 3.3. If any patch is good, I'll backport it for the older versions.