This thread (Import from Bookends) has a lot of background information, although not just focussed on your problem.
Search for Zotero on the forum gives a lot of posts.
Anyway, just index your Zotero folder to your database; my history with working in Zotero and in Devonthink and in a dedicated PDF reader are great. After all, Devonthink is the main part in the system that can retrieve everything.