Some Options to Consider
You can still use Kindle’s file conversion service, but Amazon has what amounts to a disclaimer that says: conversions of PDF to Kindle files, or even DOCX to Kindle is experimental. In other words, the document may not look right after it is converted, but it will work, more or less.
Another option is to use the ebook management software called Calibre. It is important to note that there is no need to convert a file to Kindle’s native format (.azw) to enable Kindle to read it. Once the file is in any of the supported formats (.azw, .txt, .mobi, .prc, .mp3 etc.) Kindle can read the file. You can also use PdftoePub as you would Calibre.
As was stated before, the conversion process is not always straightforward, in that some PDFs have such complex formatting, so much so that the user may need to help the software to properly process the file with conversion rules. To make the process less cumbersome, Calibre does have predefined rules that can handle some of the more popular types of conversion hurdles.
However, if you have a conversion job that doesn’t have complex formatting, converting from PDF to a Kindle supported format will simply be a matter of opening the software, uploading the file, specifying the output format, and hitting the convert button.