I'm not sure if it does actually affect Debug builds, as I made a Release build with these set.

symbol_level = 2
remove_webcore_debug_symbols = false

And then.

$ chrome/tools/build/linux/make_zip DIR

Traceback (most recent call last):      
  File "chrome/tools/build/make_zip.py", line 51, in <module>
    sys.exit(main(sys.argv[1:]))
  File "chrome/tools/build/make_zip.py", line 45, in main
    output.write(os.path.join(build_dir, f), f)
  File "/usr/lib/python2.7/zipfile.py", line 1141, in write
    self._writecheck(zinfo)
  File "/usr/lib/python2.7/zipfile.py", line 1106, in _writecheck
    raise LargeZipFile("Filesize would require ZIP64 extensions")
zipfile.LargeZipFile: Filesize would require ZIP64 extensions

The fix is simple.

diff --git a/chrome/tools/build/make_zip.py b/chrome/tools/build/make_zip.py
index 81e411e..4694b0c 100755
--- a/chrome/tools/build/make_zip.py
+++ b/chrome/tools/build/make_zip.py
@@ -38,7 +38,7 @@ def main(args):
     return 1
 
   with zipfile.ZipFile(output_file, mode = 'w',
-      compression = zipfile.ZIP_DEFLATED) as output:
+      compression = zipfile.ZIP_DEFLATED, allowZip64 = True) as output:
     for f in files:
       sys.stdout.write("%s\r" % f[:40].ljust(40, ' '))
       sys.stdout.flush()

Note that the ZIP file is then only about 1GB in size.