i went ahead and ordered 2 new relays, it is a cheap investment
Having extra relays is a good thing, but bad relays won't cause the lights to flash when you take it off the sidestand. That's the alarm doing that. You can still start the bike if you enter your code via the t/s switches. The procedure is in your manual.
Doesn't a sportster flash its lights when it throws a code? That is what I thought, so I would think the relays being bad could cuase a low battery which would cuase them to flash. That seems to have been my experience.