Things we've thought of, particularly considering their health situation, include making sure his ducks are in a row to keep it out of probate should their health take a bad turn (we've verified his corporation technically still owns the property and he's all the officers), still getting an appraisal within 30 days (it will also still be valid for the lender). 

Are all bank loans to the corporation documented?

I left the corporate world because I was tired of someone else telling me there was a ceiling on my income.

That is fine if all you are doing is flipping, but since you mentioned that you have buy and holds you want to make sure that you don't lose the tax benefits of rentals.To avoid having the dealer status attach to you personally, I would consider doing the flipping through an S-corporation. 

A year or two later the mortgage company realizes what you've done and demands you take the property out of the S Corp or they're going to call the mortgage. 

Rarely, they will even bother with these offers.If it was a wealthy owner it will be owned by a corporation, or a llc so something is not quite right.

It's funny, I've grown up in REI all my life, and in a way that lead to me not appreciating the value of it as a business; but after 5 years of startup/corporate life my eyes finally opened to how powerful it is, thanks to my friend, @Ryan Mapes. 

If you haven't made a corporate election for the SMLLC, it is disregarded for federal tax purposes and all activities and assets of the SMLLC are dissolved into the activities and assets of the owner.For California, it appears you are managing the LLC from California. 

However, it only protects you from one type of liability: accidents.After that you want to compartmentalize your assets, which is often accomplished through the use of LLCs or corporations.

My question is that if I purchase real estate through my S-corp (or create a different LLC/s-corp to purchase real estate) would that look like a loss/ expense in terms of my overall income from the S-corp and therefore lower my AGI?