I misread your original post... You won't be able to import. That'll do exactly what your seeing - all new records.
You're going to need to design a custom DTS package. It will need to read the source file, get the record id, attempt to read the 2nd file, if found update the record, if not append the record to the table. I'm about to go start a system shutdown for monthly maintenance, and will be heading out after that. But PM me your email address and I'll see if I can't remember to get you a stripped down version of what we do in the dts package tommorrow morning. BTW, we import to a temp table in the database for speed then process from there to the real table. We found it to was quicker - don't ask why, we just accepted it.