If you are talking about board exams merit list, then in the CBSE main 5 subjects are taken into consideration for preparation of merit list. While if the candidate has failed one of the five main subjects and did appear for any additional subject, then its additional subject's marks will be taken in place of failed subject's marks for preparation of merit list and also for calculating aggregate percentage marks.

All boards have their own criteria, to be board specific, you may visit that particular website of that particular board and find out the relevant information. Generally, boards consider all the main subjects and if a student fails in one of the main subjects, then additional subject and the aggregate percentage marks are calculated and  thus on the basis of aggregate percentage, merit list is prepared.

Hope it helps.