I have been using MaemoMapper and it will break my SD card filesystem sometimes. Mostly when I am downloading map images.
Cards are always formatted for Windows FAT filesystem and that will cause problems on Linux OS. N800 (and 770) do not have any tools to check card filesystems and repair it. So connecting card to Windows (or desktop Linux) and checking card there should fix it. But only way to fix broken card is to format it into FAT32 on PC.
I just upgraded my N800 firmware, let's see if it works any better. And if it does not work any better should I buy any bigger SD cards for N800? Then I would have more data to be destroyed.