Is there any reason to go ahead and get the Stage 1 ECU re-flash if I'm not changing the pipes anytime soon?

I understand that the bike will run a little richer and a little cooler.

I have an '07 Super Glide.

 

I had the stage1 flash and SE filter done when I bought my bike. I rode it that way for about three weeks with the stock exhaust and it ran great so I dont think you are going to hurt anything. I think the general consensus thoughis to skip the download and go with one of the several tunning devices that are available.