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It appears you have answered your own question. Throughout the string, it is agreed an appraiser needs to own the first physical conditions report within the second appraisal (simple disclosure). However, I am not sure you can EA away anything.
Agree, can not (imo) EA the first report away.
Here is something else I am not sure of which you appear to be alluding to. So correct me if I am wrong. It is my opinion, the second report was standard procedure. The first report (which provided core samples) is actually above and beyond what is generally seen. My point is I am not convinced the second is substandard. What is convincing is the first report appears more credible. This may be splitting straws but none the less true.
You are saying ordering a less in depth inspection report is standard procedure commercial properties or foreclosure sellers ? That may be the case, but it is not applicable now to this assignment.
The extraordinary assumption could be something as simple as "had xxxx company inspected the subject under ideal conditions the report would yield similar results". As a group, we have no idea how the second engineering firm will respond. It is not unusual to have dueling reports. Whether they are related to the physical condition or the valuation of the property, reconciliation is a major part of commercial appraising. This reconciliation is done in the third step of the assignment.
You said in first sentence you are not sure can EA away ! The fact is client ordered two reports, the first was more complete, end of story. Stuck with it. Have to disclose the first report was done and what results are, and how it might affect MV , because MV assumes a well informed buyer- who might become aware of/order a complete inspection report. Either provide two values, or disclose
Here is what I do not get from many of the comments (not yours exclusively). That somehow the lender is going to cherry-pick the report and place the most desirable ones in the file? This begs the question of how is this possible without being caught? There are appraisal orders, emails, and checks paid for services. Further, such behavior would be a felony on the banker's part, it does not make sense to me as to why some believe this could happen. And most of all how is this the appraisers' responsibility?
We can not anticipate, nor be responsible for, what a lender will do. It does not matter what the lender does /or which report they use - we are responsible for what WE do in the appraisal, and we can not be, or appear to be, deceptive/misleading in our appraisal , no matter which inspection we base a value on. Since so many of your peers are seeing an issue imo that is valid feedback