I encountered a similar issue almost at the same time last week using the same workflow. I have had this workflow on my Alfred (current v. 4.8) for years and never had any issues until last week.
The only folder listed in my "Search Scope" was "~" (preceded by a folder icon). I removed that folder so that there are no folders in my search scope (the text below the scope table says if it the search scope table is empty it will use Alfred's default search scope). The search feature began working again.
Not sure if that is related to the same issue that you are experiencing. You mentioned above:
Wondering if the "~" is creating issues?
Just a thought...