Master-Update dates from the days of punch
cards. I post it here fairly often (!) which may illustrate how when your favorite tool is a hammer all problems look like nails. Call our two data sources A and B ...
You might think of A as your database master and B as your update file. You'd only have to select the key from the database, not the whole record, to figure out whether each file record is already on database. It could be a relatively large query, but only one and outside any of your update transactions.