Ok. I understand a bit more now.
Let's start from the beginning.
How does the data get to you? .csv format, external database?
What I'm getting at here is: The data must be coming from some place and it is constantly changing.
The easiest way to do what you're saying is get in touch with the people who manage that data, and ask them to create an audit trail and dump that data daily to you. So that way, every day you are getting a file with only those things that have been added or changed in some way.
Say you get an audit file like this:
ID, Type, Field, OldValue, NewValue
1, Change, someField, 0, 1
2, NewRecord, someField1, ,10
2, NewRecord, someField2, ,15
2, NewRecord, someField3, ,9.9
You can create queries that say
"Anything that says Change, perform that change on Table2"
"Anything that says NewRecord, loop through the fields given and add those values to their respective places in Table2"