As I read it, you didn't complete the assignment per the terms of the engagement and you didn't provide a competently developed "as is".
From the client's perspective you didn't complete the assignment competently, and based on your questions it appears you weren't competent to develop an "as is" because you're here asking people how to do it and challenging some of the responses.
There's no point in getting fragile over a lender offering suggestions on how to solve a situation that you didn't solve in your report. We wouldn't take it personally if a borrower or a broker did it; we would just blow it off and proceed to do what we are supposed to do.
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In any case, here's the answer on the "how to": The typical buyer for this property who would have closed their sale as of that date and with the structure in that "as is" condition might not even be an owner-user and that property might not even qualify for SFR financing at premium terms. The buyer might be a contractor or investor who will intend to complete the roof and flip the property for a profit. So no, "cost to cure" will probably not cover the market's reaction to those conditions. You should anticipate to find a discount consisting of "cost+contingencies+profit" which will exceed the cost to cure.
The way you would develop such a discount would be to START with the costs and then figure out what such investors expect in terms of profit. One way to do that would be to find flips where you can figure out what the difference was between the initial acquisition vs the subsequent resale. Figure out how much they spent - aka the costs - to do the rehab/remodel. From there, the equation amounts to [resale price - (acquisition+costs) = profit margin]. Find several examples of heavy fixers or flips to find the before/after and figure out how much these investors expect. If they spend $5K to fix a cracked slab or redo the finish on a pool then how much extra beyond that $5K do they clear upon resale?
You're not looking for direct comps for your SC grid; you're looking for matched pairs (beater vs finished) from which to extract the adjustment factor. Then you import the adjustment factor in for use with the direct comps in your SC grid.
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BTW, all RE is local; but in my region the discounts frequently amounts to "cost x 2". If they spend $75k on a remodel they expect to clear another $75k to offset their contingencies, their nobody-works-for-free and their opportunity costs for whatever resources it took to acquire, hold and market the project. If the roof is the only element and the cost is less than $5k then - based on what I've seen in the past - I would anticipate the discount to be more than cost x 2 due to the small cost involved, so perhaps cost x3 or cost x4.
Regardless of the above, you need to look at the market data for fixers and develop your own opinion as opposed to taking our word for anything. You're trying the emulate the market's reaction to these attributes, not ours'.