This investor claimed to have a special standing that allowed him to be able to buy the note for about 50 cents on the dollar. 

What I would like to do as some have done in residential is to purchase wholesale, rehab with cash and do a cash-out refinance after all work is completely and completely rented.

Our business partner also believes if we don’t sell the house in the two week time period before the asbestos abatement is completed, we have lost nothing and we can move forward with the sale of the home with the asbestos problem resolved.Whaddya think ?

That would be my first question unless you just plan to quit claim the home into an LLC after you have closed on the refinance. 

Our firm completes cost segregation studies however a $600k apartment building doesn't typically justify the cost of completing a study. 

:-)If he has legitimate deductions he should claim them whether he has received a 1098 or not.

Maybe you do 2 at a time, and it takes you 4 months to complete the process.

But they will need to see bank statements and even credit score info before moving forward, you will have to submit for draws during the rehab, and they will hold some of the $$ back until the rehab is complete to their satisfaction.Bottom line is as an investor (from your perspective, not the lender's), you should always have the cash saved and available to fund either type of deal without having to take a loan from another source. 

Is everything changed to your name through the deed/title, or is there separate paper work that must be completed

I think it depends on location, quality of rehab work completed and if the home was properly remediate (TDI certificates, etc.)