If you engage the half nuts on your mark a couple of inches out from the start of the cut, any backlash in the lead screw will be taken up as it "drags" the carriage along the bed. i.e. the lead screw will be in the same position at the start of the cut.
Best thing to do is not to disengage the half nuts. However if your lathe has no reverse and you don't fancy turning the spindle backwards for twenty turns, there is another way.
Set up a back stop for the saddle (piece of MS bar against the tail stock?), put a mark on the chuck. So you are ready, wind the saddle back against the stop, when the mark on the chuck comes up to to the top, look for your number and engage the half nuts. The saddle position will be locked to the gear train like it was last time. At the end of the cut, disengage the half nuts, retract the tool, wind the saddle back for the next cut.
I invented this method when I was cutting a 5 1/3 TPI thread, the first two cuts were great, the third was a new thread. i believe its because of the fact that your number can drop into the lead screw at any position so for a 4 TPI lead screw, its every 1/4" in travel, the problem is if you thread is not a sub multiple of 1/4", the angular position of the chuck can be anything.
Frank