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Not that this helps you out now to recover, but when I travel even for a few days, I have Calibre and my complete library on a netbook, as well as the full library stored in the cloud, just in case something goes wrong where I might need to do a complete factory reset after the reader freezes, database corruption, etc.
I never use the SDcard on the reader since I only keep around 400 books on it at a time, so I also carry at least that many books on a spare SDcard I keep in my wallet with spare camera batteries, etc. With Kobo's track record of introducing more bugs in new firmware, I'd also never let it update while I'm away, just to avoid having to reset it all up just in case there was a really annoying bug that wouldn't let me read.
But with those precautions, you could get set back up as long as you even had wi-fi (unless that Kobo reader you have will only setup through a PC, but I didn't any were that limited if they're wi-fi capable). Short of damaging or losing your reader, you can recover.
And Murphy's Law seems to then take over then at least for me. Because I'm ready to recover from even a forced factory reset, nothing has ever gone wrong for me yet while I'm away.
I'll admit it's really odd that it wiped all your books from the reader, unless it somehow also did a factory reset (which you could tell by checking which firmware is on the reader). Even if the database gets corrupt, logging out of the Kobo account and back in usually takes care of that and it will rebuild a new database from the existing books still left on the reader.
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