The current zipFile implementation supports the allowZip64,which can make large zip files.
There is a bug in the current implementation of close method ,where the extra field is overwritten .

To reproduce it :
1.Create a directory with more then 4 GB of data(spread over many files).
2.Make the zip of those files using the any rar achiever which adds NTFS metadata(mtime,atime and ctime) of files in the zip.
3.Apped a new file to the zip using the zip library .

When i open the zip again ,the files processed after the ZIP64_LIMIT is reached will have there extra fields overwritten.

I have attached the zip which contained the python used to add the new file, and the images of zip archive before adding new files and after.

The issue stems from the following code inside the 
def _write_end_record(self): method ,where the extra fields are trimmed .

if zinfo.header_offset > ZIP64_LIMIT:
    extra.append(zinfo.header_offset)
    header_offset = 0xffffffff
else:
    header_offset = zinfo.header_offset

extra_data = zinfo.extra
min_version = 0
if extra:
    # Append a ZIP64 field to the extra's
    extra_data = _strip_extra(extra_data, (1,))
    extra_data = struct.pack(
        '<HH' + 'Q'*len(extra),
        1, 8*len(extra), *extra) + extra_data

min_version = ZIP64_VERSION

I was looking at `zipfile._strip_extra` trying to figure out how it works. It doesn't. It skips extra headers after the last one that matches. That's what causes this issue.

Here's a fixed version:

def _strip_extra(extra, xids):
    # Remove Extra Fields with specified IDs.
    unpack = _EXTRA_FIELD_STRUCT.unpack
    modified = False
    buffer = []
    start = i = 0
    while i + 4 <= len(extra):
        xid, xlen = unpack(extra[i : i + 4])
        j = i + 4 + xlen
        if xid in xids:
            if i != start:
                buffer.append(extra[start : i])
            start = j
            modified = True
        i = j
    if i != start:
        buffer.append(extra[start : i])
    if not modified:
        return extra
    return b''.join(buffer)

Or this one, easier to understand:

def _strip_extra(extra, xids):
    # Remove Extra Fields with specified IDs.
    unpack = _EXTRA_FIELD_STRUCT.unpack
    modified = False
    buffer = []
    i = 0
    while i + 4 <= len(extra):
        xid, xlen = unpack(extra[i : i + 4])
        j = i + 4 + xlen
        if xid in xids:
            modified = True
        else:
            buffer.append(extra[i : j])
        i = j
    if not modified:
        return extra
    return b''.join(buffer)

Not sure which one is better.