We need to know more about your current or likely file structure to provide any real detail. However,
If you are tracking records at the phone number level, you could do an import which updates existing records based on the DNC phone numbers as the match field to set a flag field in your table for the DNC field. This need not change any data except the DNC flag field itself.
Wouldn't it be possible to run a script monthly to compare each record to the DNC list and if it finds a match, to flag the record as DNC?