When we mask flat file through FDM by applying a where condition, masking is not retains non masking rows.
Example: masking with condition where ID not in ('A','Z') are not shows up the rows of A and Z id.
Release : 4.9
This is an expected functionality of FDM masking. When you apply where condition on fixed width masking file, masking file will be generated with the records only that at are masked.