We also have a number of lists having list items with one or more attachments. In our case, we enabled the OOTB entity extraction to produce some additional refiners. If you have enabled entity extraction on the "body" managed property, entity extraction will fail on any list item with an attachment and that list item and its attachments will NOT be indexed, and as a result, will not appear in search results.
Microsoft is in the process of developing a hotfix for this. When we successfully apply it, I will post our results