very simple script for burning in reliably (hopefully) subtitles into the mkv and converting them to .mp4 ! This script needs HandbrakeCLI in path variables or in the same directory. You can download it from here: https://handbrake.fr/downloads2.php

handbrake.bat

@echo off
:: The Command and conversion is copy&pasted from the Internet and I only added the subtitle command and the for loop....
:: if it's givin you an error delete the ">>log.txt" (didn't test if it's working but it should echo everything into a file called "log.txt")
:: You can delete the Lines starting with "::" (they are ignored)

for %%i in (*.mkv *.avi) do (
HandBrakeCLI -i "%%i" -o "%%~ni.mp4" -e x264  -q 20.0 -a 1 -E faac -B 160 -6 dpl2 -R Auto -D 0.0 --audio-copy-mask aac,ac3,dtshd,dts,mp3 --audio-fallback ffac3 -f mp4 --loose-anamorphic --modulus 2 -m --x264-preset veryfast --h264-profile main --h264-level 4.0 -s "1,2,3,4,5,6" --subtitle-burned
rm -f "%%i"
)>>log.txt

pause
exit