Use a pre-trigger in Calibre Interactive to delete the MASK SVDB DIRECTORY prior to the main run.
Use a consistent naming scheme for that directory ( like svdb ); there is no Trigger Parameter for it.
Example for LVS:
In Setup > Preferences > Triggers set the Calibre Pre-Execution Trigger field to:
rm -rf svdb
Now when Run LVS is used the svdb directory will be deleted immediately before nmLVS is launched.
For more on Triggers see the Calibre Interactive and Calibre RVE User's Manual section "Setting Calibre Interactive Internal Triggers".