Nine times out of ten you'll get away with it. The tenth, you'll curse, because you've bricked the Kobo. Sometimes it will need a few presses on the hard reset button. Occasionally it will do a Lazarus impersonation if you let the battery run flat, and then plug in and restart with the hard reset button, and cycle the hard reset a couple of dozen times.
And when all else fails, you can, if you're of a geekish turn of mind, Google for hacker forums and find out how to download an image of the system drive, and install it on the internal memory card.
But I don't do Linux at all, and I don't really feel like downloading and installing the necessary tools on my elderly and increasingly unreliable XP box, and then spending a stressful few hours wrestling stuff into submission before I can use my tiny e-ink reader again. Not when my data on this device is toast anyway, and a new one is only thirty quid. The time I'd probably need to spend is worth more than that. So I'm putting a few links here for later, when I feel like conducting surgery, and called into Smiths on my way home last night. The shiny new one is indeed shiny, because they only had the white/silver version in stock.
The Mini snapbacks (and a lot of other Kobo accessories) have been drastically reduced, so I've also bought a nice purple snapback. This is because at some point I will probably fix the old one, and then it's going to be used for the books I don't want on the device that gets handed to the Aged Parents when they want to borrow a book. Purple seems a nice discreet colour-coded reminder for "this is the one with the porn on it." :-)
Some useful links for cloning a working card for backup or to to put into the old device:
Mirror of http://julesjones.dreamwidth.org/274933.h