While you can’t run a search based on the byte information of a file, you can run a search for other properties such as entry name and even the file size. Assuming that these identical entries have the same entry name, you can definitely use workflow to automate creating shortcuts to these documents. You would first have to figure out which one of those is the original document, then have the workflow delete all the other duplicates and create a new shortcut from the original document. I mocked up a quick workflow and was able to get it to work. I’ve attached a screenshot of the workflow I used to help you get started.

I hope that helped. Please let us know if you have any additional questions!