I communicate with owners when there's a change in their income stream or when I need their permission to do something.

John If primary residency you can claim the tax exemption, but need to report rental income and pay taxes for that. 

And a cashed check and deposit into your account.   

How much income is being produced2.

Are there any benefits or incentives to our church maintaining the building and partnering with someone to do something creative with it such as a rental to low income/unhoused, food pantry, stoarge, etc? 

I am happy to reimburse her when the accounting is satisfactory and I can see what was done and apply it to a line item.

Does your partner want to take a big chunk of the losses (depreciation) to offset income?

You could use some of the rent collected in the duplex to increase your income basis.

Also, if you are qualifying for the loan based on your personal DTI (debt to income ratio), the personal loan could change those ratios and keep you from then qualifying for the mortgage you want.

I have a house, no kids, good income, no debt.