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The Mobi file format doesn't support "right-to-left" languages, so there's probably not a lot you can do about this.
If your device supports the more capable AZW3 format, try using that instead; it does have RTL support.
How well Calibre will convert it is an entirely different question; PDF is the worst possible choice of starting format for conversion, and it often works poorly. The best way to convert PDF into another format is generally to use a decent OCR application.
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