Yes, your 12th class scores matter in the selection process for the course of IPM from IIM Indore as the eligibility for the IPM course is to have at least 60% aggregate in the 10th and 12th class for the General and OBC category and at least 55% aggregate for the student falling under the SC/ST category.
Once this eligibility is fulfilled, there's no need for the 10th or 12th class marks. Then you will have an entrance followed by the GD and PI round.