@Gta: You should have no problem putting the update on the device using a MAC. Taking the card out is not needed unless you are having problems other than the ones you have mentioned. The MAC should mount the device and let you access it. Just copy the contents of the update package into the ".kobo" directory on the device.
If you have the card out, you don't want to format it. One partition is safe to be formatted, but, that will lose any books on it and mean a setup will be done when you disconnect.
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