As others have mentioned you can do a cost segregation on whatever you'd like. 

Do you offer the service of doing a cost segregation study?

It's two seperate transactions for tax purposes,  neither one changing the outcome of the other just because they occured at the same time... in theory it would probably be better to simply have the amount of the commission deducted from closing costs if at all possible, but if compensation was already being offered througu listing broker, it is what it is.

You should have had a conversation with an accountant prior to going ahead with the cost segregation study.A cost segregation study breaks down a building to more components than just building and land.

Hi there,I'm trying to determine the best way to live in and eventually acquire a property as an inheritance while maximizing cost-effectiveness.

Looking my insurance policy it mentions that I can opt for settlement under Actual Cash Value vs Replacement Cost. 

That’s a small fraction of what all that would cost in my market.

The main reason is that it is not initially set up for a Real Estate business like other “real estate-specific” accounting software.

Also with cost seg how it now affects the way I actually file on those two properties.

This is the first time I have done something like this, where it was for other reasons besides not paying rent.