[Liisachan]

you can try something like this example
test.bat
---
FOR %%f IN (*.mkv) DO (mkvmerge -o "new\%%f" --no-attachments "%%f")
---

EDIT (FIX)
I forgot to quote the last %%f, which doesn't work if a file name has a space, "%%f" should work in such a case too. The example above will transmux every MKV file in the current folder and write new files in the sub-folder "new". --no-attachments is just an example, where attachments will be dropped in newly created MKVs. One can replace this part with what they actually want to do.