Hi,
If you're getting the data from SFTP it would be good to split the data into few files at the source and load them into ACS. Maybe you can use external signal to trigger second data import workflow once the 1st import done. This way you will be able to troubleshoot any issues happens during data import and if there's any network glitches you may avoid endup re-running with full set of profiles again. Also you may consider running during non-business hours, if your system used for daily marketing activities.
Thanks!
Thanks, Sathees