The section 5 Declaration is a means of getting a definitive from the local authority on whether something does or does not constitute exempted development.
From -
http://www.irishstatutebook.ie/2000/en/act/pub/0030/sec0005.html
5.—(1) If any question arises as to what, in any particular case, is or is not development or is or is not exempted development within the meaning of this Act, any person may, on payment of the prescribed fee, request in writing from the relevant planning authority a declaration on that question, and that person shall provide to the planning authority any information necessary to enable the authority to make its decision on the matter.
In and of itself, it has no power to amend previously permitted plans.
It may offer clarity as to whether or not the omission of an extension would constitute development within the meaning of the act.
In your case the question to be asked is a different question, since what you're doing is the opposite of development, its leaving something out.
One question might be:
"If I chose to vary the permitted works, must this be ratified under the planning the development acts through the mechanism of a revised planning application?"
However, you could ask a totally different question.
List all the works you want to have carried out (minus the extension) and then ask -
"Does this constitute development under the planning and development act 2000 and in particular section 4(1)(h) or is it exempted development?"
If you have to seek permission, you could just get it for the works you want to do, omitting the extension.
ONQ.
[broken link removed]
All advice on AAM is remote from the situation and cannot be relied upon as a defence or support - in and of itself - should legal action be taken.
Competent legal and building professionals should be asked to advise in Real Life with rights to inspect and issue reports on the matters at hand.