You will have to reinstall the channel. If you were using a forwarder all you would have to do is swap out the .dol. You can get the new updated channel from here. My updater did not seem to work online either, maybe because we have full channels instead of forwarders. Not sure if it can change the dol on the nand....just speculating on that.
That is from the gx website. I assume that it is not capable of writing to the nand.Note that there should be an update_path option at the loader's settings to give the directory you want to use for the update,
in case you don't use the default one :/apps/usbloader_gx/, and a setting to be able to update to the latest beta revision