You will need 2 data flows:
- Pull one file into a database table
- Read 2nd file. Use Table_comparison transform to do the comparison. Make sure to select Detect deleted row(s) from comparison table. Add a Map_Operation transform to reset the row types to normal and set the I/D/U flag. You can write the results to a table or a file.
Check Table_comparison transform: comparison method settings and performance impact in a nutshell for more details on performance implications.