RE: Construction Process for Comp over Slate.
Determine the proximate cause of the leaks and proceed from there. For this discussion, I am assuming that the cause is wind and secondary causes are that the wind uncovered the previously damaged slate.
As you mentioned, the slate is in very bad condition so it will not serve as a solid underlayment for a new layer of composition shingles and should not have served as the current underlayment for the current layer. However, the original underlayment may be gap decking and forced the composition shingle roofers to use the solid slate surface instead of tearing off the slate. Furthermore, the old/original decking will probably incur much damage throughout the demo process and not be able to be reused (this is where coverage for rot can be gray and when coverage is gray, you will most certainly pay).
It appears that you have chosen to tear out the composition, slate, and repair any of the original decking (assuming that is the last layer) and replace with slate as the underlayment and comp. as the top layer. Essentially, you just paid the insured for two (2)roofs. What would you do if the insured had 2, or 5, or more layers of composition roofing? Would it be any different than if they had 3 layers of slate, 3 layers of metal, and 4 layers of comp? It shouldn't be and you need to advise the insured that they got a great deal.
I wouldn't sweat too much over the construction process of applying comp over slate, since it likely won't be happening in this case. If in the Vieux Carre district, officials will ensure that compliance is met. Is this claim in New Orleans?
RE: Depreciation.
Without commenting on the language of the HO8 policy, it appears that the biggest issue this claim is faced with is that of depreciation. Based on the facts given, I'll bet you are right on the money with your estimated amount of depreciation. However, proceed with caution as some courts construe unreasonable levels of depreciation as bad faith. Being "reasonable" and "right" are often completely different- especially depending on the area where you are working on your claims.
As a general rule, when depreciating past 50%, make sure that you document the age of the present material and are depreciating against the useful life of the material costs only. As you may gather, I recommend using the straight line depreciation method. If you are depreciating against the material and labor costs, you will increase the risk of heavier legal scrutiny. If the carrier requires that labor be depreciatied anyway, document that and save your assetts. Make sure that your depreciation is "reasonable" in that it allows the insured a reasonable allowance for recovery.
RE: Lagniappe.
If this claim is in New Orleans or South Louisiana, you may suggest to the homeowner or property owner that they seek assistance through the Louisiana Recovery Authority (LRA). Further assistance to the owner will be made in writing up all of the damage so that they may relay their loss estimate to their CPA (don't give them tax advice, just tell them to show their estimate to their CPA).