My check engine light goes out when I crank the Bike (Heritage Softail FLSTCI) and after a couple of seconds it comes back on. What does it mean?

 

Take it to your mechanic!

 

is it throwing any codes?

 

If it does...duck!!

 

It's seeing some kind of a failure developing and it may (or may not) have already thrown a code. By your description, it sounds like my bike behaved when the stator began to go out. After starting the light would go out, then come back on for a couple of seconds and go out again. At that time it hadn't yet thrown a code. About a month later I was riding and the light came on and stayed on. When I got home it had thrown a code, which led to a stator replacement..

 

I agree; if the light stays on and ECM is working properly it will throw a code.

My "check engine light" turned out to be the voltage regulator, but the code could have certainly be related to a defective stator.

I swapped the regulator first only because that job was easy and from what I had read the OEM regulator's are junk and will go out eventually anyway.

Turned out the new regulator fixed my problem.
BTW- I highly recommend Cycle Electric regulators.