Paying NYT and Apple for NYT subscriptions - help!

I just realized that I have been paying double for my New York Times News Crosswords and Cooking subscription. I already have a direct all-access subscription to NY Times since but have also apparently been paying Apple for Crosswords and Cooking. My Apple ID email address is the same one I used for direct subscription to NY Times. NY Times says they only see one subscription (my direct one) and said to call Apple I did and they see I have manually canceled my subscription but don't seem to be able to get that email address unhitched from the Apple version of the accounts. Has anyone else dealt with this and been able to successfully resolve?