Thanks for clarifying that, cack. I definitely took the other meaning, which shows the benefit of spelling out an answer, doesn't it? We could have gone a few reply cycles tossing that one back and forth. LOL! Well done!
Okay, different tack.
Exempted development is just that. Exempted development is development you can carry out without permission. When you have permission you are supposed to carry out the development in accordance with the plans and particulars lodged. Some local authorities have interpreted this to mean that once a permission is granted it "fixes" things in position and that even otherwise exempted development, if a permission "rules" on it, is not now exempted.
There are counter arguments, of course, but it may be an uphill struggle and involve a lot of time and money.
In the present situation as you have clarified it, a retention permissions seems the cleanest way out and I would strongly recommend you ditch the engineer and appoint an architect with planning permission expertise to deal with this matter. A court battle over three small windows is pointless and could end up costing you thousands of Euro for appearances, research time and solicitors fees to defend a position which the court might find is indefensible.
That's not to assume that this is the only issue that may arise with your premises or that you are 'entitled' to get the permission. We offer advice on AAM in the presence of unknowns so please read my signature file disclaimer and proceed with foresight and caution.
ONQ.
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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.