There is a big difference between a block with 0 values and an empty block with #missing values.
If you want to get rid of the 0 values, you have to run a calc script which sets them to #missing. Something like actuals = (actuals/actuals)*actuals; . There are examples in this forum.
If you want to get rid of the #missing blocks and this is a structural problem (you can not change the script for some reason), then you can do a housekeeping task in the maintenance window. This would involve to export all data and then clear the database and as last step a data load of the export file.
The best thing is to avoid this from happening, but this would be something very specific to your situation.