First off, if it's "like for like", why are you thinking about changing the way that the wiring is protected? If it's in EMT, run the new stuff in EMT.
Secondly, if I read your post correctly, you're intending that there won't be a permit pulled for working on a fire alarm system in a high rise building.
For the first, ask the AHJ; for the second, don't even think about it. Go through the correct channels, get a permit, get it inspected and do right.
