Hi, I've been messing around with DSLinux and came up with this. It'll use dosfsck to check or repair your filesystem when it gets messed up. I've only tested it on a Supercard SD but in theory it should work on anything that supports DLDI.
Sorry for the crappy download link but I don't have anywhere to put stuff online at the moment.
Don't forget to dldi patch, use at your own risk etc etc