I think leaving the half nuts engaged will negate any worries with backlash, therefore the cutting tip should run in the exact same place. I only say this because I got much better and more consistent results.
Its not leadscrew backlash you need to worry about - its all those gears between the leadscrew and the spindle - it could be significant which would put the new cut thread out of 'step' with the cutter? But at the end of the day - whatever works for you, do it!
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