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As far as I am aware you have to go to the dealer if you've lost a key, replaced a key or changed the ECU. They can invalidate the lost key registration in the ECU with an adapter.

Why do you want to bypass it?
How do I bypass the immobilizer system on my 2012 ninja 1000

Taken from z1000 service manual pages 16-98, 16-99, etc.:

" Immobilizer System (Equipped Models), ZR1000DB ∼/EB ∼

This motorcycle is equipped with an immobilizer system to protect the motorcycle from theft. This
system provides a theft proof device by means of matching a code between the inbuilt key transponder
and ECU (Electronic Control Unit). If the code does not match, ignition system, injectors, subthrottle
valve actuator and exhaust butterfly valve actuator will not operate and the engine will not start.

Abstract

•Do not keep more than one immobilizer key of any system on a key ring. Jamming of the key code
signal may occur and the operation of the system may be affected.

•The warning indicator light (LED) will flash for a period of 24 hours once the ignition switch has been
switched off and the key removed. This flashing can be set to on or off as desired by holding the
left and right buttons down for two seconds within twenty seconds of switching the ignition off.

•If all coded keys are lost the ECU and ignition switch will have to be replaced.

•The immobilizer system can not function until the ignition key code is registered in the ECU.

•A total of five keys can be registered in the ECU at any one time.

Operational Cautions

1. Do not put two keys of any immobilizer system on the same key ring.
2. Do not submerge any key in water.
3. Do not expose any key to excessively high temperature.
4. Do not place any key close to magnet.
5. Do not place a heavy item on any key.
6. Do not grind any key or alter its shape.
7. Do not disassemble the plastic part of any key.
8. Do not drop the key and/or apply any shocks to the key.
9. When a ignition key is lost, the user should go to his dealer to invalidate the lost key registration
in the ECU.
10.When the all ignition key is lost, the user should go to his dealer and have a new ECU installed. "
and register the ignition keys.

No.9 and 10 are strongly recommended to the customer to ensure security of the motorcycle.

Key Registration

Case 1: When the ignition key has been lost or additional spare ignition key is required.

•Prepare a new spare ignition key.
*Cut the key in accordance with the shape of the current ignition key.
•Remove: Rear Seat (see Rear Seat Removal in the Frame chapter)
•Remove the immobilizer/Kawasaki diagnostic system connector cap [A].
• Connect the key registration adapter [A] and key registration unit .

Special Tools - Key Registration Unit: 57001-1582
Key Registration Adapter: 57001-1746

•Insert the registered ignition key into the ignition switch, and turn it to ON.

Verified
○The warning indicator light (LED) and the immobilizer warning symbol [A] blink to display the registration mode
(go to the next step)

Not Verified
○The warning indicator light (LED) and the immobilizer warning symbol [A] blink to display the collation error
(refer to the following failure illustrations).


etc..."
 
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