I used to have the same problem with PDF files on my Kindle Paperwhite. What worked for me was to convert the PDF to PS and then back to PDF.
On linux:
$ pdftops MyScannedPDF.pdf
$ ps2pdf MyScannedPDF.ps
Now no more missing characters (at least on Kindle Paperwhite)!!
(as pointed out by member
isachummel on
this thread)