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Take the Brackets '[]' out of -ss time and clip time and designate a correct output folder:
for %%a in (*mkv) Do ffmpeg -i "%%a" -ss 00:00:20 -t 30 "c:\pathToOutputFolder\NewName_%%a"
or
for %%a in (*mkv) Do ffmpeg -i "%%a" -ss 00:00:20 -t 30 "c:\pathToOutputFolder\%%a"
HOWEVER, if you are cutting at a non Key Frame, You may get junk that is unplayable. The latest ffmpegs allow cutting at Key frames but
you must specify the exact frame time (e.g. 00.00.20.040). It is possible but unlikely that all your MKV files have a key frame at the same location
so batch cutting would result in unknown results.
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