Hi Gavin, I appreciate that this happened a few years back, but I've had exactly the same thing happen to my bike. Can I ask when they replaced the engine under warranty, did they say anything about the air filter mod you've done to your bike? I've done something similar and removed the air box replacing it with a cone filter so I just wondered whether they mentioned it at all? Also did you have to take the bike to an approved RE service centre or could you choose where you had the work done?
Thanks in advance for your help.