First it is important to know the reason behind adding the additional stamp duty later on. If the reason is valid then yes it can be added by mentioning the details of partnership including that it is a part of an existing agreement. For instance by mistake if agreement is made on stamp paper of lesser amount then the actually needed then one can add an additional stamp paper. If the reason is increasing the capital or add/remove partner then the supplementary agreement is to be made and additional stamp duty is to be paid on such supplementary agreement.
Feel free to contact LegalWiz.in for any Partnership Registration or changes in partnership agreement.