A)had been operating at a loss in the 1990s, it had become profitable in 2006, and would continue
looks good. past perfect is ok, since the SW announced - already in the past, and she describes something that happened before she announced.
would continue - perfectly fine to describe a future event in the past.
B)had been operating at a loss in the 1990s, although becoming profitable in 2006, and will continue
will continue - incorrect.
C)had been operating at a loss in the 1990s, it became profitable in 2006, continuing
continuing - ing modifier that modifies the clause - this is illogical to use here. the fact that it became profitable in 2006 will result in high profits at least until 2025? no.
D)operated at a loss in the 1990s, becoming profitable in 2006, then would continue
becoming now acts as an ing modifier. the fact that the lab operated at loss in 1990 resulted in becoming profitable in 2006? this is non-sense.
E)operated at a loss in the 1990s, becoming profitable in 2006, and continuing
same as in D.
A is the best.