Script that is an adaption of the code found at http://n2.nabble.com/Loss-of-local-file-links-td2209604.html It adds a Local-File field to the BibTeX file with the relative path of the referenced file.

gistfile1.py

#!/usr/bin/env python
""" Add/update Local-File field to BibDesk-organized BibTeX file """
import sys
import base64
import re
import shutil
from Foundation import *

key_pattern = re.compile(r'^(?P<indent>\s*)Bdsk-File-1 = \{(?P<key>.*)\}[,}]$')


def decode_bdisk(key):
    """Return the relative path of file referenced by key """
    decodedBytes = base64.b64decode(key)
    nsData = NSData.dataWithBytes_length_(decodedBytes, len(decodedBytes))
    plist, fmt, error \
    = NSPropertyListSerialization\
      .propertyListFromData_mutabilityOption_format_errorDescription_(\
      nsData, 0, None, None)
    if plist is None:
        print "key: %s" % key
        print "failed to decode archive due to error: %s" % (error)
        exit(1)
    # currently an implementation detail; may not be at position 6 in future
    if (len(plist["$objects"]) > 6):
        return plist["$objects"][6]
    else:
        print "unknown format for property list %s" % (str(plist))

file = sys.argv[1]
backup = "%s~" % file
shutil.copy(file, backup)
out = open(file, 'w')
for line in open(backup):
    key_match = key_pattern.search(line)
    if key_match:
        out.write("%sLocal-File = {%s},\n"
                  % (key_match.group('indent'),
                     decode_bdisk(key_match.group('key'))))
    if not re.search("^\s*Local-File = ", line):
        out.write(line)

Foundation comes from pyobjc.