I assume you want to make a BD out of the MKV ... that would be Re-authoring and is not what CloneBD is intended for.Can you please add a function to import MKV aswell.
Kind Regards.
When converting Blu-Ray/4K UHD to mkv with example MakeMKV or MKVToolNix you will get an .mkv as output.
Is usefull that there is a way to import it in CloneBD when for example you can't find you're disk and have mkv as backup on harddrive.
So without everytime if you want to convert something you need to look where the freaking discs are because harddrive is usally easyer to find and ofcourse can store more.
That's why i think is usefull to have an mkv import option inside the program aswell.
I second what Coopervid suggested.You can use the free TSMuxer and export as BD ISO, BD folder or m2ts. Of course nothing with menus like cartman208 already told you.