Please read the section 12(1), 49(3) with 187C carefully. The purpose of keeping a nominee ( in case of private co) is to maintain the minimum no. of shareholders prescribed u/s 12(1).
Your query is not very clear. Please specify whether target company is a pvt co or public? And what exactly is the shareholding of another company?
If its a pvt co, you cannot revoke that nomination and make 100% shareholding to a single shareholder. Take Declaration from Ostensible Owner in form-I (i.e. Director holding one share) and from Beneficial Owner in Form II (Holding Company)within 30 days of approval of transfer (from the date of Board Meeting of Subsidiary) and file form 22B (By the Subsidiary) within 30 days of receipt of Forms I and II. This form 22B shall be filed to ROC.