Hi Chariot
First of all please do not treat anything you read here as professional opinion, many of us who use this internet chat room are happy to give our views freely but it is always off the top of our heads rather than considered advice. Your question is fairly wide ranging and has numerous scenarios which, if any of us was to give a professional opinion, would require careful consideration and research to reach a balanced and justifiable conclusion.
Shooting from the hip I would suggest that there are at least three scenarios here-
1- the individual private dwellings within which the contractors are working - the Fire Safety Order does not apply within the dwelling even whilst contractors are working there as the house is still occupied and therefore primarily domestic premises. The HASAWA certainly applies in respect the duty of care by employers and employees, contractors and sub contractors. Part 2 of the CDM Regulations will apply, and perhaps part 3 if the project is notifiable. I would think that the premises are still primarily dwellings rather than a construction site.
2- The Communal Areas of the blocks of flats- the Fire Safety Order will apply, the fire risk assessment may require review due to the variations in fire risk that may arise in connection with the work as you point out. If the flats are occupied during the works the FSO and the CDM Regs relating to fire will be enforced by the fire and rescue service. The H&SAWA, and the CDM Regulations will apply.
3-I would expect that in such a project the storage and welfare compounds will be dealt with in their own right rather than as you say taking the whole estate into account. Again an interpretation will need to be made as to whether these compounds constitute a construction site.
There is some useful information available on the HSE website but this tends to focus on construction matters and is very scant on advice in respect of the Fire Safety Order. I assume you have researched the HSE website and have a copy of the current ACOP L144.
Please do not rely on any of the above, I have put it forward hoping to prompt discussion through which many if us may benefit.