You want to convert to the encoding that your database is using.
'man iconv' explains how use iconv.
..and..
iconv -l
..states the available encodings.
http://linuxcommand.org/man_pages/pdftotext1.html
..mentions that the default text output is LATIN1 encoding, but that you can also specify the output to be another encoding using '-enc encoding-name'.
If the db is encoded in UNICODE, then try outputting pdftotext in UNICODE.
If pdftotext still outputs encoding with gremlins, consider processing the pdftotext output with iconv using the '-c' flag, since it silently removes characters that are not convertible to the '-t' encoding.
iconv and pdftotext should be accessible from the shell, so you can run some test cases to help determine what might work.
cheers,
Torben
