So what are they going to do with the second set of wafers then considering they ran into rather large issues? Would that be a scrap?
No-one knows.
The 5,000 chips they have on hand (suspected to be 4,000 now because wafer 2 is the one which returned the crappy power results) won't fill very many orders. The next 6 wafers were supposed to be completed once testing was completed on the first 6 but no-one seems to be talking about when they'll be completed any more (it was supposed to be only a few weeks after the first 6 wafers were done).
Perhaps more importantly, no-one's talking about the bulk order for 63,000 chips - from which the majority of pre-orders were likely going to be filled.
This leaves a lot of uncertainty about when customers who ordered after August can expect delivery because it doesn't sound like they're going to have the chips on hand to fill those orders any time soon even if they can manage to get sub-spec units out to June/July pre-orders in the next month.
I think people who are hanging in hoping that BFL will ship "soon" are assuming that once they start shipping everything will be fine. But BFL has actually said nothing recently which suggests that they have enough components on hand to fill anything except the very early pre-orders. Those with orders placed after August really need to start asking questions about what's happening with the bulk chips because delivery of their orders could still be months away even if June/July orders get filled soon.
They should also know with absolute certainty by now how many of each unit they are going to produce from batch 1 (which affects the likelihood of a particular order being filled from batch 1 because of their stupid 1/3 shipping plan), but that's something else they're not disclosing.