Locate segments

Locate the start and end of the segments you want to delete

$ ffmpeg -y -ss 00:25:53.30 -i abc.mkv -frames:v 1 out.jpg
$ ffmpeg -y -ss 00:25:59.28 -i abc.mkv -frames:v 1 out.jpg

Segment to delete: 00:25:53.30 to 00:25:59.28

Create segments

Create segments a and c (the video without the segments you want to delete)

$ ffmpeg -i abc.mkv -map 0 -c copy -t 00:25:53.30 a.mkv
$ ffmpeg -ss 00:25:59.28 -i abc.mkv -map 0 -c copy c.mkv

Join segments

Create a file listing the segments created previously

$ cat files.txt
file 'a.mkv'
file 'c.mkv'

Concatenate the segments

$ ffmpeg -f concat -i files.txt -map 0 -c copy ac.mkv