Nintendo has acknowledged this bug and is now offering a fix, according to MTV. Just don't expect that fix to be convenient.

For the price of free, Nintendo is offering to fix all glitched save game files in the most ridiculous way possible: by asking you to send your SD card to Japan. Yeah, that Japan, and specifically this address:
Nintendo Service Center "Metroid Other M" Dept
56 Kaguraden Ogura-cho
Uji, Kyoto 611-0042
Japan
Now, I know what you're thinking. "They can't be serious," you say. Trust me, I thought this was an April Fools joke at first, but then I looked at my calendar and realized that it's nearly October. (I also need to take my cat to the vet at 4pm.) This, unfortunately, is an actual solution for a bug on a console that does not support traditional means of fixes via fancy things like "patches" and "title updates."
It goes almost without saying, but if you're stuck with a borked save, think real long and hard about how much that lost time means to you, because, and I'm guessing here, you're not going to see that SD card for a while. I suppose, though, that you could pass that extra time writing angry messages about Other M on the Internet. I heard that's all the rage these days.



















So console patches don't sound so bad now...
My thoughts exactly.
Also, it's not just the SD Card. People can choose to send an SD card with a copy of their save or their actual console. That's nuts. Imagine if you had to ship your PS3 back to get a save game issue with Warhawk or whatever fixed?