Jasper,
Do you mean a change of use or a material alteration? Forgive me if I am teaching you how to suck eggs, a Material Alteration is internal alterations to the layout, refurbishments, etc (the explanation of a material alteration is just too damn long to detail fully!!!), whereas a Material Change of Use occurs when a building changes its use (office to shop, shop to residential, etc.)
If the building is existing and an alteration has taken place, the benchmark for Building Regulations compliance is that the level of compliance is no worse than it was prior to the works commencing. This can result in many scenarios, even more so with the introduction of the RRO, that could demonstrate compliance with the Building Regulations but fall foul on a fire risk assessment.
There is now a conflict due to the dynamic status of the RRO and the approach of the Bulding Regs which is a bit more flexible towards existing situations.
Any decent Building Control Body (BCB) should advise the client/architect that compliance with regs can be achieved, but would also advise them where issues may still exist regarding fire safety.
The only scenario I can possible percieve where this may be okay is BS5588 Part 11 Clause 10 - Small premises, but there are a lot of issues/restrictions to consider.
I think this is a problem that we will be seeing increase on internal alterations work, the provisions in Regulation 16B for provision of fire safety information should address changes of use and extension/new build works, and create a bit of synergy between the two processes.