That is why it is important to have contingency plans a solid agreement in place before entering the purchase of the property.Your options are to buy him out yourself or raise cash to buy him out. 

We are buying the house with cash, no contingencies under a LLC name.

Additional contingencies should be added to the budget and discounted valuations should be applied in such scenarios. 

Anything can happen: the market can shift, we can go into another extended lockout period, the property can be destroyed by a natural disaster or by vandalism, the list of contingencies is endless.

Since the vacancy is required for the loan, this would fall under the loan contingency.

This way, you would be paying for the roof as part of the property purchase, allowing you to claim the tax depreciation once you take ownership.Delayed Closing with Roof ContingencyAnother approach is to add a contingency to the closing that allows you to replace the roof before closing but delays the actual closing until after the roof is installed and insurance is in place.

Then what happens in that case, what other contingency and deals between the two parties can be analyzed further ?

I don't believe that you can get a specific contingency on vacant space for CRE, but typical due diligence is 60-90 days with 1 or multiple 30 day extensions. 

I’ve gotten in the habit of offering cash with few or no contingencies then refinancing after closing/ seasoning period.

I attribute this to the legal system and more specifically contingent fee representation most plaintiff's rely upon.