I don't know if it's entirely too late for a response. Been a bit busy. :-)
Non-profit organizations aren't really my area, but no one else has answered this, so I'll say as much as I can.
First, non-profit does NOT mean the company is at break-even and has no profit. It means it's not in business for the purpose of making a profit for its owners. Its purpose is something charitable, educational, cultural, etc. rather than commercial. Cash flow and net income are two different things, and it's common for companies to keep profits in the company to use for various things. In this case, you need the cash flow for a mortgage payment. How would you have any cash flow to pay the loan if the company doesn't have more coming in than they are paying out? i.e. you're allowed to have profits that serve the purpose of the organization and to run. You need to make the loan payments, so having profit to cover those payments is fine. You're even allowed to pay reasonable salaries. (Not everyone has to be a volunteer.)
I know there are limits on what can be considered non-profit, and l know there's limits on those salaries (something of controversy), and limits on the amount of profit and its uses. Since that's not my area, I don't know these details. But paying a loan is certainly a reasonable use of profits. If you really want more details about all this, I'd suggest you find an accountant who has some expertise in this area.
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