Certain Canadian Yamaha bikes ( SuperTenere,FJR1300, R1 and a few others I believe)employ an imobilizer system with 2 chipped keys and a 3rd Red code re-registering key, D NOT LOOSE THIS RED KEY !! It's only US bikes that DO NOT have the imobilizer system and chipped keys.
I live in Canada and have both a 2006 FJR1300 and a 2014 SuperTenere , both have chipped keys, the on-board imobilizer system will NOT allow more that 2 chipped keys to be registered at any time , as soon as you register a 3rd key, it will automatically un-register the 1st key that was originally registered and so on, so if you lose the 2nd key that was originally registered, and register a new key,the system will automatically cancel that 1st key, you just have to re-register that 1st key to have 2 operational keys.
I personally don't like this system, it doesn't prevent bike theft, thieves will just toss the bike in a cube van and speed off in 30 seconds , then strip it for parts! It only prevents a drive away with a copied standard key, highly unlikely !
This system adds costs and huge risks of lost keys, if you lose all 3 keys , your screwed !, all new $50 keys,locks, imobilizer system, ECU, about $2500 repairs!!