Hi Alex,

> I guess there is somehing wrong with the channel mapping, but without the
> fliter_complex the mapping seems to be okay.

I think the filter_complex messes up the mapping. Note this mapping
from your output:
> Stream mapping:
>   Stream #0:2 (pcm_s24le) -> atrim
>   atrim -> Stream #0:0 (pcm_s24le)
>   Stream #0:0 -> #0:1 (copy)

and this result:
> Output #0, mxf, to 'test_new.mxf':
>     Stream #0:0: Audio: pcm_s24le, 48000 Hz, mono, s32 (24 bit), 1152 kb/s
>     Stream #0:1: Video: mpeg2video, yuv422p, 1920x1080 [SAR 1:1 DAR 16:9],

and this warning:
> [mxf @ 00000000003b69c0] there must be exactly one video stream and it must 
> be the first one

I'm sure that's your issue. The filter seems to be messing up the
mapping, at least in this automatic case.

Instead of

> C:\>ffmpeg -i test.mxf -vcodec copy -map 0:v -acodec pcm_s24le -map 0:1 -map 
> 0:2 -filter_complex "[a:1]atrim=start=0.035" test_new.mxf

you probably need something like

ffmpeg -i test.mxf -vcodec copy -map 0:v -acodec pcm_s24le -map 0:1 
-filter_complex "[a:1]atrim=start=0.035[ashifted]" -map "[ashifted]" 
test_new.mxf

(Untested) Note that I'm trying to explicitly map the filter output to
a particular stream, avoiding automatic mapping. You may have to play
around a bit more with the map options.

Is this a bug, BTW? Documentation on "-map" states:
>    The first -map option on the command line specifies the source for
>    output stream 0, the second -map option specifies the source for
>    output stream 1, etc.

Digging further, documentation of "-filter_complex" clarifies:
>    Output link labels are referred to with ‘-map’. Unlabeled outputs
>    are added to the first output file.

So the first documentation section is somewhat unclear, as it is
"disturbed" by the second behavior. (And in the second section: "first
output file" -> "first output stream", right?)

Moritz
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