I don't know anything specifically about Access, but this sounds like it would be a LOT easier in the form of a Database rather than spreadsheets. Instead of sending a complete DB refresh you would make updates and inserts as needed to the DB. You can also keep a column with a date and timestamp in it to know exactly when the corresponding email has been sent.

You could have the whole thing from start to end as a single DB, or make an intermediary step of sending data between sites/businesses as CSV and then parsed into a new DB at the second site/business.