I’m coming late to this–and have not tested it yet, but did find an interesting workflow that may do what you are wanting:
1.5.1 Zotfile Preferences
Steps for setting up file organisation if you’re using a cloud to link files into zotero
- Go to Zotero → Tools → Zotfile Preferences
- In general settings, you can tell zotfile where to store your documents. For this, in “Location of Files”, choose Custom Location, and choose the folder you selected in 1.2 (in my case, “ZoteroAttachments”)
- You can choose to have zotfile sub-categorise your files in this folder, using these wildcards. Many people choose to categorise by Author (%a) or year (%y).
- I prefer organising my files by subject, so I pick %c, meaning collection. You can also combine different wildcards, like so: “/%c/%a” (Screenshot 07). The wildcards will create folders with the entirety of the field referred to. In my case, it will create a folder with the name of the collection in Storage (/ZoteroAttachments/CollectionName)
If I’m reading step 4 correctly, your PDFs will be stored in folders with the name of the collection you have assigned them to–which could then be indexed in DT.