I'm afraid you need to research a bit more. A quick google search led me to this page:
https://robotsfuckyeahalloneword.svb...n-on-kobo-mini
Which has instructions to modify the SD card from the Dropbox image you're using to make it compatible with your Kobo Mini.
Instructions are based on a linux host as they're using dd. You might want to try them on a VM.
Since managing hardware across a host/VM is harder I would suggest to make images from your original SD as well as the new debian SD card using the windows software you want and copy these images to the linux VM. Then use dd directly on the images. When you're done copy the new created image to your windows host and flash it on a SD using win32diskimager again.
Have fun!