There are many powerful capabilities in LVS-RVE to help with debug. The command line execution of LVS should give you the same debug capabilities as LVS invoked from Calibre Interactive. Very important will be the rule file statement "MASK SVDB DIRECTORY svdb QUERY" (or some variation of that statement as you desire).
Here's a link for some quick reference information about working with LVS results in RVE:
Thanks alot Chris. I was looking for exactly same thing. It would make my job easier now ( previously i used to debug the LVS using extracted netlist now RVE will be easier and time saving )