I have done this only once, and it was not by choice but out of necessity. Not an easy task. By no means this is recommended by Docuware. Make a good database backup and take all Docuware services down
The reason the sync is not working is that GUIDs of both FCs are the same.
So you'd need to change the GUID of the FC on one of the systems. This only can be done directly in dwsystem database. I suggest you install a sql tool that allows you to search for a value within the whole database and replace it with a new value.
You'd also need to make the same change in two tables in dwdata. Also, rename file at a root folder of each of the FC disks.