Here's the problem as I see it. The Indigos that are available now are the descendants of relatively few legally held snakes when they went under protection in the 1970's. Not everyone back then kept scrupulous breeding records so very little information is available for most of the Indigos out there. Add that to the fact that people have bought and sold snakes sometimes several times before the snake finally ended up with someone who actually bred it. Many times (probably the majority of times), the actual lineage of the snake is unknown. The only thing that you might know is the fairly recent lineage, maybe one or two or at most three generations.
However, if you buy a baby from Breeder "A", you can ask him where his snakes came from. He can tell you that he got them from Breeder "B". Now you know that you should probably see Breeder "C" to find a mate (and inquire where his came from) unless Breeder "A" or Breeder "B" is working with multiple bloodlines (some are).
The good thing is that most of the people breeding Indigos are not in it to make a quick buck (yeah, like there was a quick buck to make in it), and they do care about the animals and the future of the lines available. All of those on this forum do and are honest to the best of their knowledge about lineage and breeding.
I think the best we can do is to take whatever information we presently have and go forward with that. There may be some small amount of inadvertent inward breeding that happens, but at least it won't be direct parent-offspring or sibling-sibling. There should be enough diversity in available couperi and erebennus bloodlines that if we are careful we can keep them far enough apart to insure plenty of reasonably unrelated gene pool for future breeding.
The one where we may run into issues is rubidus. There just doesn't seem to be a whole lot of those around.