Best way to work with interlaced and progressive clips in the same timeline

I´m shooting with Sony MC-50E camera in 1920x1080, 50i. When importing with Log & Transfer I can work with ProRes 422 files in interlaced mode. I have to mix the footage with video screencapture which is progressive (ProRes 422). The final videos are for web only so it should end up as progressive H264 videos. I´m getting good result if exporting to H264, 1024x576 with deinterlacing enabled, but exporting to full HD gives typical interlaced lines in the picture. How can I avoid this and what is the best solution for working with both interlaced and progressive clips?

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When you're ready to export your sequence, use Quicktime Movie, Current Settings, Self-contained. Take that file to Compressor to transcode back to h.264.
The Apple T.V. preset is very good.

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Best way to work with interlaced and progressive clips in the same timeline

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