Security problem, Immobilizer locked the car

My son's 99 Honda Prelude had a bad ECU. The car could run with it but not properly. So he bought a used ECU and replaced the original. The problem is
that the immobilizer, now, doesn't let the car start with either ECU.
Is there a way to reset or deactivate the immobilizer?
Thank you
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Can the dealer make a new key if you bring to them the car's key and the VIN of the car from which the new ECM was removed? This way maybe they could make the key and get the code for the replacing ECU.
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VIN
According to the Service Manual for my 99 lude, the immobilizer can store up to 5 key codes. When learning a new key, the dealer uses their PGM Tester to rewrite the immobilizer and needs all the coded keys including the red LEARNING key. Furthermore, "if someone tries to start the engine with the learning key, all master and valet keys must be relearned." Maybe that's why the original ECM doesn't start the car now. I saw that warning when I bought the car, never opened the package, and filed that key safely away.
The last note about substituting a known good ECM is that it must be rewritten with the PGM Tester. Since I've never had this done, I'm not sure if the original and substitute red LEARNING keys are needed for this procedure or if they're generic.
Bottom line, it sounds like you will be able to reuse your expensive original keys with help from the dealer.
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He did not use the red key, just tryed to start the car with the regular one.

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As was said you are in for a trip to the dealer to program your keys in the immobilizer system....

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