You have stated that you have already filed a civil suit and as the defendant has not filed the written statement, hence the court has taken action recording that written statement not filed by defendant.
Now you are asking opinion from this forum as to whether you can add additional prayers at the stage of evidence for demolition as well as for declaration of title.
Before answering your question you should clarify that what is the nature of suit you have filed and what was the relief sought in the suit filed by you?
Basically your father was not having clear and marketable title on his name because he acquired the property by an unregistered document hence it is a defective title.
You have also stated that subsequently he constructed a house over the vacant land, if so, whether he obtained permission or approval from municipality or any competent authority for building construction plan?
If no approval for construction was obtained then the building constructed itself would be considered as an illegal structure and liable to be demolished if the authorities issue a legal notice and take legal aciton.
You have also stated that your father transferred the property to your name by a gift deed, it is also not known if he had executed a registered gift deed or transferred the property by an unregistered gift deed, whatever, your father's title to the property is defective hence your title is also defective.
Now you say that your neighbor has encroached some portion of your property, in that case you have to prove that the encroached portion belongs to you by a substantial documentary evidence i.e., by a registered document on your father's name.
In the absence of any registered document on your father's name, in the civil suit, he should have prayed for declaration of title on his name on the basis of the unregistered sale deed and posession and enjoyment for over three decades and he should produce the said document besides utility bills and the revenue records on his name. The subsequent prayer should be for mandatory injunction against the defendant to demolish the encroached portion and delivery of possession of the encroached portion of the property.
If that was not done, then you can file an amendment petiiton to amend the suit accordinly.
You can discuss in detail with your advocate and proceed as suggested