• So is the source file missing data (i.e. are the lines of empty fields supposed to have data) or just extra lines.

    If you are happy that the data is complete, I would

    1) raise a defect against the file source to get the null rows removed

    2) apply the conditional split as per Phils suggestion to ignore them - the exact rules for the CS will be down to you and the nature of the data (I would find a field or combination of fields that CANNOT be null and validate against them)