The car's remote locking and it's immobiliser are separate systems with different methods of recognising a key. Every remote generates a unique code sequence also each key contains a separate unique immobiliser id chip number which is not related to the remote code, only the pattern of the blade was the same until your locks were replaced.
Suppose the original remotes A and B had been paired to the car, when remotes C and D were paired the earliest one A should have been bumped out leaving the car accepting B, C & D, but maybe you now possessed A,C & D - by adding A again the car should accept C, D & A if the Mk2 s the same as the earlier cars by only remembering the last three remotes to be paired.
The key's unique immobiliser chip number is read and verified when inserted into the steering column lock. It requires Honda Diagnostic Software to change the learnt codes by writing them into the car's memory, the procedure has the on screen menu name 'rewrite keys' and should erase all learnt immobiliser codes and register the new ones presented at the time.
The auto locksmith has ensured the missing key will not turn the ignition or disable the immobiliser, and it's remote code should now be forgotten.
e.g.
Your keys Remote cypher Immobiliser-ID Blade pattern
Original A F9rhK2GjjCPaWx 519204527384 723910
Original B iYe8T3x0iEu3Qm 830471395261 723910
New C eTm2Wi8GSo9aeW 274905871282 479458
New D nWy7ER5xDKLp9v 432857092167 479458
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TG