I resolved my own issue after talking with COAMS from Nortel. If you try to delete child script references from the Master Script during busy hours in Symposium, the script reference may appear like it is removed from the Master Script, however, the database still hangs on to the reference and you are not able to deactivate the child script. You will get a message stating "Unable to deactivate script. It is being referenced/pending delete by another script. (something close to that)
The resolution is to stop the TFE service (Traffic Flow Executor) on the Symposium Server and start it again. (do not do during business hours when Symposium is working).
Stopping the service and restarting will release the reference of the child script from its parent. You can then deactivate the child script and delete it as necessary.