It seems the afdust adjustments job uses different scripts, so use of the run settings file isn’t supported for that particular script. Instead, at the bottom of the script that runs the afdust adjustments (Annual_afdust_adj_12US1_…), change:
$RUNSCRIPTS/emf/afdust_adj_emf.csh $REGION_ABBREV -m “$RUN_MONTHS” $SPINUP_DURATION
to:
$RUNSCRIPTS/emf/afdust_adj_emf_customdates.csh $REGION_ABBREV -m “$RUN_MONTHS” $SPINUP_DURATION
That should automatically skip any day where there is not a METCRO2D.