Currently the upgrade process is do-or-die -- if it fails, you'll need to restore your database and files area from backup and try again. Currently, only the OJS 2.x to 3.x migration renames the files in the files area, but that part of the upgrade script can't currently be run separately. If there are problems moving files during the upgrade, they should be logged so you're aware.
If you're interested in how the renames happen, it's implemented here: https://github.com/pkp/ojs/blob/ojs-3_0_2-0/classes/install/Upgrade.inc.php#L855
Public Knowledge Project Team