I have a 04 honda foreman rubicon 500, polarity accidently reversed, will this effect the ecm?

 

Normally, when you swap batteries or put a charger on, you have ignition switched off, and the bike blows the main fuse as soon as you touch the terminals the wrong way, after which the whole system is dead. So the ECU doesn't get a dose of the wrong polarity unless the ignition was switched on when you connected the battery wrongly. In contrast, the regulator is permanently connected (via the fuse) and it is sending power the wrong way through it that blows the main fuse, so the regulator may have been damaged.