Rivnuts from Homestead, PA on 4/4/2019 7:28:08 PM:
Along the GAP portion of the trail between Pittsburgh and Cumberland there are large groceries along the trail in Homestead, Connellsville and Cumberland. There is a smaller grocery in Confluence. There are dollar stores and convenience stores in Boston, Meyersdale and Frostburg albeit somewhat off the trail and up/down hill(Frostburg/Meyersdale) from the trail. The latter may not provide the breadth of products to suit your gluten-free diet however.
I don't know specifics along the C&O as well but, in general, the options are fewer and further off the trail. However, I'll defer to others that know the towns along the C&O better than I to provide more info on food options there.