You must issue a strongly worded legal notice to the concerned 3rd floor owner enunciating the fact that you have access rights to the terrace for water tanks. As you have mentioned, you got the roof right with the latest amendment. Even though water is an easementry right of an individual, no one can restrict that despite being on private property. You should file a suit for an injunction for easementry rights and access to the terrace before the district judge.
The roof comes under the common area and cannot be sold or put to exclusive use by any flat owner. You can file a civil suit in court to obtain common law rights. Roofs have common rights on land, each having a 1/3rd share each. It is illegal to use a room and toilet for common use. If the roof top was sold prior to the roof right being given to you, then the dealer had no competence to give you any right on the roof top in the first place.
Your remedy is to file a criminal fraud complaint against the merchant and have an FIR registered against them. Unless your sales invoice is revised, it is not possible to form an opinion on whether to claim the rights to the roof.
Reference: RERA – 202100499-20210043-13229