right now this causes many level 2 warnings about looking in another file for this variable. The run eventually succeeds since CarpetIOHDF5 silently continues if it is unable to read anything at all for a given variable (ie. it only aborts if a variable is read only partially but not if it is not read a all since it is missing from the fileset).
The attached patch marks these variables as being fully read the same way the ignored variables are handled and adds some further checks if the reader is called from the FilerReader rather than from recovery.
The do_inVars logic (explained in the source) is to possibly read a variable if either do_inVars == NULL (corresponds to "all" variables) or do_inVars[vindex] != 0 (which can be positive or negative). As it is right now I think the later checks that end in "continue" are now superfluous.