What hardening will not do
- It will not overwrite a hostile
.htaccessthat it cannot safely replace. - Rotating salts is off unless explicitly enabled; salt values are never logged.
- It will not run through the Connector plugin. Clean and harden need SSH.
PROTECT also adds a baseline (inventory snapshot) and monitor (added/modified/deleted vs that snapshot). Unexpected changes are a verdict, not an automatic rollback.
Use hardening after cleanup, or on a clean site you want to keep that way. See FAQ.