Anything that re-encodes the video (to a non lossless format) is going to potentially sacrifice the quality.
FFMpeg does a great job with it, and there is a gui for it that offers a ton of options (including rotating the video) with a program called WinFF: http://winff.org/html_new/
I have tried FFMpeg and didn't do it. It actually rotated the video 180 degrees in one of the tests. And I don't see any rotate options in Handbrake (10.2.286).
I ended up saving the original file alongside the converted one, just in case.
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