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I have a Video #1, it has audio. Also I have a Video #2, with audio too. I would like to concat the #1 and #2 (or play #1 first, and then #2) and then add a watermark in #1 for the rest of the video, preserving audio timestamps.

I used this command but the watermark appears on the #2 video?

ffmpeg -i Video1.mp4 -i Video2.mp4 -i watermark.png
   -filter_complex
       "[1][2]overlay=5:5[v2];
        [0][0:a][v2][1:a]concat=n=2:v=1:a=1"
   -c:v libx264 -crf 21 -c:a aac -b:a 384k -ar 48000 -movflags  faststart Out.mp4
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Concatenate can be found from this link

In case of using same codec

!echo "file 'video_1.mp4'" > list.txt
!echo "file 'video_2.mp4'" >> list.txt

Add watermark at (x=1, y=1) coordinated

!ffmpeg -y -f concat -safe 0 -i list.txt -i watermark.png -filter_complex "overlay=1:1" output.mp4

I don't quite understand your description, but i think it fits your title.

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