Help needed please. I have a 06 Honda Civic. Alternator just been replaced then had flat battery. Battery replaced and now won’t start, flashing green light on dash, had someone out to program new key (not sure if he knew what he was doing) said it’s not my key it’s the fuse, had a new fuse replaced for the key fuse no luck. Don’t really want to throw much more money at the car until I no it will fix it. Any suggestions that you.
I repair a lot of these systems so maybe I can offer a little direction. I'm not sure any of it is DIY other then checking all your fuses and I also do not think many poorly trained locksmiths would do well either. You need a real auto smith or tech who specializes in automotive electronics and has decent diag/programming tools. Autel 908 or H.D.S will make short work of the job.
It could be a couple things causing the issue. Here is what I mostly run into for these symptoms.
Low battery or poor connections: IF your battery is too low or has a poor connection your modules may not be receiving enough juice to turn on. Honda's like to do this when battery is below 11V
Key lost programming: This happens often with low batteries or connecting/disconnecting the cars battery. Not sure why this happens but its usually related to the "password" shared between the key and the immobilizer module (receiver). Simply reprogramming the key would fix this.
IMMO,MUX and/or ECM has lost synchronization: This is also very common for the same reason as #1 but what happens here is the check code between one of the three gets corrupted. The key is still programmed to the immobilizer but the immobilizer can not verify with the ecm or mux. This requires a similar but different process then just programming keys.
ECM,IMMO or MUX is Offline: Either lack of power from fuse, shorted internal components or corruption in flash programming has shut the module down. This is not usually the case but I have run into it on many occasions none the less. Generally its the ecm. This is easily tested just by seeing if the systems are accessible with a scan tool. If they are then probably ok.
Below is the "how it works" from Honda for your 2006 Civic