My checklist would probably go something like this:
tax issues (as you described)
concerns about potential preferential treatment of an insider
concerns about whether a refund could materially impair the charity’s operations (and be seen as a breach of the public trust or a fiduciary duty)
checking to confirm that the refund wouldn’t make the charity close-to-insolvent (this is the only scenario I see in which a suit by a non-governmental actor seems plausible—if the charity ended up unable to pay other obligations, the refund could be a constructive fraudulent conveyance)
donor bankruptcy issues (as described in my top-level comment)
Or problems with the state charity regulator.
My checklist would probably go something like this:
tax issues (as you described)
concerns about potential preferential treatment of an insider
concerns about whether a refund could materially impair the charity’s operations (and be seen as a breach of the public trust or a fiduciary duty)
checking to confirm that the refund wouldn’t make the charity close-to-insolvent (this is the only scenario I see in which a suit by a non-governmental actor seems plausible—if the charity ended up unable to pay other obligations, the refund could be a constructive fraudulent conveyance)
donor bankruptcy issues (as described in my top-level comment)