A Benefit Cost Transfer was previously processed for a paycheck. I am now submitting a Salary Cost Transfer for that same paycheck. Will the Salary Cost Transfer take into account the previously processed BCT when redistributing assessments?

No. The Salary Cost Transfer will simply reverse the assessments based on the earnings in that transaction and reassess based on those earnings. In this case, you will need to submit a new Benefit Cost Transfer to reverse the actions of your previous Benefit Cost Transfer.