I'm not surprised they can't work it out - its a very confusing piece of legislation.
It relates to Part L1 of the Building Control Act which deals with conservation of energy. Having read it several times over, I'm still not 100% sure. However: -
Section 2 is the relevant section - it deals with Work on existing buildings. It goes on to define what constitutes 'building work' is, and then goes on further to define what a 'Material Alteration' in a building is (para 2.4). I do not believe yours is a material alteration. It says 'An alteration is material for the purposes of these Regs if the work would result in a building or controlled service or fitting (e.g. boiler - my added words to explain!) which before did not comply with the relevant requirement, being more unsatisfactory in relation to such a requirement' Phew!!!!!
Since you are merely moving a boiler that does not comply (its not condensing) to the other side of the room, its not 'more unsatisfactory' - it is just the same.
Hope that helps.
Suggest you print this out and take it to your specialists who argue you need it replacing.