Yes.
For all TFS Bug Item Synchronizer versions there are tools (Rename Utility, Remove Linkage Utility) to modify internal database where these links are stored.
Starting from TFS Bug Item Synchronizer version 2.5 it is also possible to open this internal database in tool like Visual Studio and edit this same data using SQL or manually.
This is possible by installing these two:
After installing these it is possible to open and modify Defect and WorkItem tables for complex change scenarios.