Perl script which can be used with Cygwin or WSL to generate a Handbrake queue file file. My purpose was to shrink some of my handycam videos which were stored as .MP4.
You could easily create your own queue with your settings.
Choose one of your files
Select the encoding profile you want
Add to queue
Open queue
Export queue as somefile.hbq and open it
Remove xml-header and <ArrayOfQueueTask> start and end tags
Keep only your <QueueTask>...</QueueTask> with those tags and save it as task_template.xml alongside this script into the start folder from which you will start your find
This assumes you copy the task_template.xml and the script to /mnt/d/Someplace
Replace the rest of your path with ___SOURCE___ and ___DESTINATION___
The script will add the found .MP4 files (if you have others, just alter the script) to ___SOURCE___ and will add the same filename to ___DESTINATION___ as .mkv (you may alter this to your needs too).
Edit $fileDir in the script to fit your linux style start-path
Fire the script in a bash at the start-path location and it will generate a file called handbrake_final_queue.hbq
Import this file back into your handbrake queue and you should see all the jobs for all your files found under the start path.