I found this video: https://www.youtube.com/watch?v=oYAnmjT8P-E
1. Install, run, and set up Ubuntu MATE on your PI.
2. Run a live Ubuntu instance off a USB. (I guess you could use Disk Genius here on Windows but I didn't try.)
3. Copy everything in PI_BOOT to a folder.
4. Run Gparted.
5. Delete the PI_BOOT partition.
6. Shrink the PI_ROOT partition by, for example, 1 gig (I think Disk Genius can only do 512mb FAT16 partitions.)
7. Create a new FAT16 partition at the end of the disk.
8. Label it PI_BOOT.
9. Copy the files back into the PI_BOOT partition.
10. Put SD card back into Pi and it should boot up.
This means you have 64mb at the start of the SD card wasted, not a big deal. Do not move any partitions or you will break things. You don't set any flags on the PI_BOOT partition.