MySQL - Backup new and modified entries only
We have a similar process in place, where we run a script to 

TRUNCATE TABLE backupTable;
INSERT INTO backupTable SELECT * FROM mainTable WHERE datefield &gt;= xxxx


WHERE x is the time the backup ran the day before. Then we run MySQLDump against backupTable.

Alternatively you could do something similar and set a 'backedup' flag in the main table, and then just

INSERT INTO backupTable SELECT * FROM mainTable WHERE 'backedUp' = 0;


and then update the backedUp flag in the main table.