I wonder why B isn't correct in sense of tenses (i understand why it is not correct for parallelism). It is crystal clear from the sentence that the fighters had started to train long before the estimation of the rebels, as the sentence say that "trained over the past two years". As the sequence of events is absolutely clear the use of past perfect is optional but not must, that is past simple will work as well. So up to my understanding we don't necessarily need to use the past perfect
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