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Assuming that:

your file has a unique key (like some sort of account id, order id etc.)
it is sorted by that key (in ascending order)

Here is an approach that I use when working with flat...

Have you considered addinng a trigger to the DB2 database?

Glibc has an extensive hash library

See: Hash Tables (http://library.gnome.org/devel/glib/stable/glib-Hash-Tables.html)

We have a similar problem. Are you running diff? That would take forever.

Use something that has associative (hashed) arrays like awk or perl. Assuming you have several files, and an "old" one...