Marco Mc Carthy Specialist Software Support

Create a "File Cabinet Event" Auto-Index and choose the file-cabinet A as trigger, now set your conditions to activate the process.
 
In the "Match Data" section, you should pick the option "file cabinet database" and select file-cabinet B. Select the appropriate matching field(s). 
 
The "Assign Data" can remain empty, as you do not want to change any entries within your file-cabinet A.
Please note, that "File Cabinet Event" Auto-Index do not create a log output (Last Run column - in the Autoindex overview) where you could check the execution.
Therefore, you could update a status field in file-cabinet A, to show that the update was executed. (Exception for Assign Data)
 
Now in the "Write Back" section select the fields, which you would like to update / change in file-cabinet B. 

Dear Rhys Woolley, Dear Forum-Users,
Thank you for opening this thread. I have checked your question and can provide you with the following description:
KBA-36518 - How to flag duplicate documents already stored in the file cabinet
Within our Knowledge Base, we have several How-tos and other interesting guides and content that can help you with using DocuWare.
I hope the description will help you to evaluate all duplicate documents.
Kind regards
DocuWare Support