Even if the schema has changed, you should be able to edit the checks within the group, delete a check from the group, or delete the entire group.
Do you still have the original data or schema in which the Execute SQL checks were created? If yes, are you able to edit the checks or delete the group when using the original schema or data?
Using Windows Explorer, navigate to your user profile and go to your ESRI directory (Example path on a Windows 7 machine C:\Users\<user who is logged onto the machine>\AppData\Roaming\ESRI. Within the ESRI directory there is Production 10.1 folder. Rename the Production10.1 folder to Production10.1_orig. Then open ArcMap and try to edit or delete the Execute SQL checks within the RBJ. Then zip up and attach the Production10.1 folder within the ESRI directory. Perhaps an exception is being written to this location.