Have you tried Exclude Cell? I am not familiar with Calibre Interactive for DRC, but presumably it is an option somewhere in there.
Failing that, you could edit the rule file. If you want to run with Calibre Interactive (at least that is what I am taking -runset -batch to be), you'll need to find the rule file the runset calls and add the Exclude Cell line to it. Typically a rule file for Calibre Interactive is __rules__ (with two underscores each side), but if you fed in an SVRF file it might be that name surrounded by two underscores.
More details on Exclude Cell are in the SVRF manual.
you can use the layout exception command to run with partial layout
LAYOUT INPUT EXCEPTION SEVERITY MISSING_REFERENCE 1
this will make calibre to ignore the missing ref