Why are you converting them? I should think that it would be more accurate to do a side by side comparison. Unless you are planning on using a comparison tool of some sort. If you convert one or the other, then you may be masking an issue which could exist in the original conversion.
The reason for data validation is....... to check if the migration from flat files to data tables is done without any mistakes.
So, we want to ensure that the data in the flat files and the data in the SQL tables is same.
Let us validate the option "a" specified above.
Suppose there occurs a mistake or loss of some values while converting the flat files in the SQL tables (because of inherent problem in the migration tool). Then this mistake occurs again when u again convert the flat files into data tables in option "a". So, when u compare these 2 data tables, then, they both would be same (and ofcourse both will have the wrong data) in them.
So, a better option would be to use a different kind of migration tool in the second part of option "a".
i.e., first convert the files in to tables using your "application under test".
Then convert the same data files in to data tables using a different tool.
Now compare these two resultant data tables.
Option "b" is least suggested, because, of there is any mistake/data loss in converting the data tables into data files, then that leads to a false alarm.