After AI Security Incident, I Lost Some Local Files

In a recent incident, we recently dealt with a security issue involving an enterprise-level AI solution. During the remedial process, we had to revert changes, reimage some systems, as well as optimize user environments.

The security issue has been solved, but the problem is that some important files that were in the system locally and synchronized online have disappeared after doing a system cleanup. Our backups restored everything for us, though some user files and project files were not restored.

Has anyone experienced such a situation after a major security threat? Are there any methods to restore data that is normally lost in the remediation process, especially in cases of reimaged computers?