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Use FFMpegSource directly on the MKV in Avisynth, feed the resulting video into x264 (maybe using MeGUI as a front end) and you're done. Remember to handle timecodes unless you're 200% sure the video is CFR.
Also remember to check if the audio is small enough. Unless it needs reencoding, you can just source it directly from the original MKV when muxing the final file.
Also, not losing any quality is impossible with lossy encoding. The question always is how much you're willing to sacrifice for lower bitrate.
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