No not that I am aware of. I'm not quite sure if I tested your scenario correctly as I may have misunderstood it, but let me explain what I tested and then see if it matches your scenario:
1. Setup 3 Discover Scans with specific targets (\\server1\share1\, \\server1\share2\, and server1\share3) and had a group of incidents
2. Setup a Discover Scan against the root (\\server1\sharefolder\) which has the 3 folders under it (\\server1\sharefolder\share1, \\server1\sharefolder\share2, \\server1\sharefolder\share3) which had incidents
Upon doing this (step 2) the new incidents were duplicated and didn't match up with the exsiting incidents.
Let me know if i understood this correctly or not.
Jonathan