Here is a working solution if you are on a Mac and want to update the TADA68 layout.
Make your changes to the layout, compile and download the .bin file.
Click the program button on the underside of the keyboard to get it into usb drive mode.
Open up Terminal/iTerm.
cd /Volumes/TADA68\ \ / # it has some weird spacing here
ls -a
At this point, you should see a few files:
FLASH.BIN, ._.Trashes, .Trashes, .., ., .fseventsd
Now, type the following command:
cp -r ~/Downloads/FLASH.bin /Volumes/TADA86/ / \
rm -rf .Trashes/ .fseventsd/ ._.Trashes ._FLASH.bin
This copies the new layout over to the keyboard and then removes some extra files that OS X automatically creates on a USB drive when it gets mounted.
Finally, eject the TADA86 from the computer and try typing with the keyboard. At this point, it started working again for me. No need to find someone with a Windows machine.
I assume a similar issue would crop up on any variant of Linux that drops files on mounted drives automatically.