You're not supposed to use the red key as an ignition key. My understanding is it's for programming the black key during your security system setup.
Using the red key in the ignition will reset you ECU and immobilizer. So now you're going to need to go to Honda and get these items reprogrammed/replaced. You're also going to need a new set of keys.
You might be able to get away with replacement used parts, but I figure you'd have to replace everything all over again too.
From reading it sounds like you might be able to use an older ECU to get around this immobilizer, but I don't know how reliable that might be and I'm not really familiar with the system.
You might be able to find more help from Americans (just mentioning this since a lot of the forums have a lot of Americans) if you ask peope who have
Preludes. These cars appear to have the same red key available. The red keys look to also have been used in Australia.
I did manage to find this from Honda.
http://uk.answers.yahoo.com/question/index?qid=20081219115952AAnhvbW
System operation
System arms 5 seconds after switching ignition OFF. Immobilizer warning lamp flashes during this time.
Arms automatically when ignition key is removed.
Switch ignition ON.
Immobilizer warning lamp illuminates for 2-3 seconds.
If immobilizer warning lamp illuminates for 2-3 seconds then flashes rapidly:
Key code not recognised.
Remove key and try again.
Programming
When
System malfunction.
Key added or replaced.
Red master key replaced.
How
Obtain red master key and all other keys.
Immobilizer can only be programmed using diagnostic equipment.
NOTE: A maximum of 5 keys can be programmed.