Since the size of the user partition has not been changed and the part after the user partition is unused, there is no need to do any changes to the partitions. All you have to do is to truncate the image file. I do not know which tool you will use for this purpose. Just for reference, under linux you would (if the filename is KOBO-MINI.img):
truncate --size=1960838144 KOBO-MINI.img
I calculated the size from a mini image that I have. It should be the same with your image.
For writing the image to sd, I am usually using
USB Duplicator Image Writer.exe (under Windows).