Hey.
As two exams will be conducted for NEET in 2019, in order equate the scores of both the sessions, standardization techniques, psychometric methods will be used.
For the purpose of counselling  the better score of the two will be considered. Hence the exam in which you score better marks will be used for the counselling

https://www.google.co.in/amp/s/medicine.careers360.com/articles/neet%3Famp
Best of luck