Bob, there are four partners, all family members. I am sure that none of them contacted IRS. The letter reminds me of letter that 990 client (that paper filed) received  about original 990 return that was paper filed right before efile mandate for 990 returns. They responded that original return was filed and provided proof of such and copy of return. This is one of reasons that all of my business returns will now be efiled (corporate and partnership).