In general, you should avoid doing this wherever possible. Changing the course setup after the race has started is a worst-case scenario sort of situation for races that are absolute disasters.
Once the race has started, changing the timing point order will likely cause most racers to have incorrect times on the results. If it is possible to leave the crossing order as-is and hide a split time column from the results instead, you should do that.
Internally, Zone4 timing stores each racer time based on the timing point index – the racer’s individual start time is “time 0”, the first split is “time 1” and so on right through to the finish, which is whatever the index of the finish is – in a 5 lap race, the finish will just be stored as “time 5”. If you change the timing point crossing order, any racer that has a time 5 will still have the same time 5, whatever that means in the new course crossing order – and it probably won’t mean what you expected it to mean.
If you have changed the crossing order after the race start, you will need to erase all the assigned times for all racers on that course, and then re-process those racer’s times based on the new crossing order. Even this may have unexpected results, as new times will still be recorded and assigned as you are erasing and re-processing the old times.