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Digital TV uses MPEG Transport Stream, which is a container for video designed for lossy transmission, such as radio. To save CPU cycles, Personal Video Records often save the MPEG-TS stream directly to disk. The more usual MPEG is technically MPEG Program Stream, which is designed for lossless transmission, such as storage on a disk.
Since these are a container formats, it should be possible to losslessly and quickly re-code from MPEG-TS to MPEG-PS.
ffmpeg -ss "${STARTTIME}" -to "${DURATION}" -i "${FILENAME}" -ignore_unknown -map 0 -map -0:2 -c copy "${FILENAME}.mpeg"