Evacuate all non essential personal to the saucer and separate the ship, have the saucer trail behind behind the stardrive section. This way the quicker stardrive section could deal with what was ahead of them and thus protect the saucer. Also it would be more unlikely for both vehicles to be destroyed.
Unless they thought this was predestination paradox then separating the ship would not have been something they would have normally done during the first pass when the problem began.
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