Sometimes only the filesystem is damaged, and a quick format would be enough but of course a full format is always better, since some sectors may have been damaged by the Kobo. Though I'm also a longtime Linux user, I never needed formatting on Linux, but this could be a good idea.
I make regular backups of my Kobo and card contents (in tar.bz2, which is good for archives with many small files: my last saves are two ~250 Mb archives. 7zip is good also for such a storage), and if something goes wrong I overwrite the Kobo content with the save, I reformat the card and refill it with the save (both saves must be exactly contemporary). I noticed that reading and writing with the Kobo is significantly slower than with the card (which I think is not a high-end one), but I suppose that the Kobo components are rather outdated ant partially explain its hilarious slowness which remind us of the first computers with floppy disks
I also use a 4 Gb card, and I think that even a 2 Gb one would be enough, as I experienced that Calibre was not able to manage (slowly and hazardously) more than 700 ebooks (though it has been told to be able to manage 30,000, which is a typical commercial lie: you can w
rite nearly 300,000 ebooks on a 32 Gb card, but Kobo will never parse them correctly).