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Thank you for your follow-up.
First of all, congratulations on finding that check! That, by itself, is extremely strong evidence that he consented to the modification.
As for your non-profit status and your offer to negotiate, in the eyes of the law that is irrelevant. The courts generally favor settlements and offers, so that actually does not injure your claim at all. In fact it likely strengthens islt because ot can be argued he got something of value in exchange of the reduction in rent.