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I've read through several sites about transcode settings, but I can't find what I'm looking for. Is it possible to transcode a video file, changing the audio and/or video, but leaving the captions intact?

This is what I'm looking for. Virtually all my DVD rips (using MakeMKV) are in a MKV container, with MPEG2 video and default audio. The Roku supports the MKV container, and most if not all of the audio tracks, and it also supports the captions tracks. What it doesn't support is MPEG2 video. It must be in either AVC, H.264, HLS (AppleHTTP) or mpegts format. So, can we transcode the video to mpegts and leave both the audio and captions intact?

No, you cannot really include a text based captions in mpegts (on not via FFmpeg in a way the player will display them).

Thanks Zip. I was afraid that was going to be the answer.