Hi everybody, this interesting thread actually made me join the forum
Same issue for my (almost) 2 year-old Kobo Clara HD, it happened several times to found it with 0% battery and "Please recharge" warning message, despite the charge value seemed to be more than 50%. This happened with all the latest 3 or 4 firmware releases, so I think it is not associated to that. I don't use a cover too and it is set to sleep after 5 minutes.
So I investigated a bit and realized that it's discharging in a linear way until around 37%-40% and then drops to 0% and shuts down. I performed a manual factory reset after charging it to 100% (with the idea of calibrating the battery) and now testing if the issue has gone.
BTW I tried to contact Kobo support and they offered me a free replacement, still not mentioning if it would be a new or refurbished item. At the moment I haven't accepted the offer, even because I read kinda bad stories where it took weeks to get a new reader.
Any suggestions?