Sekiro uses one profile-level S0000.sl2 file, so a file replacement can roll back several in-game slots at once. The safest routine is therefore simple but strict: close the game, copy the whole account-ID directory, keep more than one dated generation, and only then experiment. Steam Cloud is another revision source; if a manual restore appears to revert itself, solve the synchronization conflict before overwriting the folder again.
Which storefront context matters
Documented Sekiro: Shadows Die Twice PC launchers/storefronts: Steam. The user-ID directory is part of the save context. Do not assume a copied S0000.sl2 belongs to the active Steam identity. The active storefront/account should be identified before any restore because cloud and local storage may not use the same path or container across editions.
Documented cloud behavior
Steam Cloud is documented. Cloud synchronization is useful for continuity, but it can also turn a restore into a conflict-resolution event. Let synchronization settle before making a manual backup, and keep an offline copy outside any folder monitored by the launcher or operating-system sync service.
Local save roots still matter
The researched local save boundary is Windows: %APPDATA%Sekiro<user-id>S0000.sl2 | Linux / Steam Play: Steam Play: <SteamLibrary-folder>/steamapps/compatdata/814380/pfx/; the known file or folder pattern is S0000.sl2. A cloud-enabled game still has concrete local data involved in ordinary play, and that local context is what you need when identifying which copy was modified most recently.
Avoid accidental overwrite loops
Copy the entire Sekiro account-ID folder with the game closed. Keep multiple dated versions because the game continually updates the same container. When restoring, close the game and launcher, preserve both the current local copy and the backup you want to test, then place the intended data in the matching profile/storefront location. Do not repeatedly open the game between different copies without noting which side the cloud client selected.
Compatibility and conflict checks
One .sl2 container can hold multiple in-game slots. File-level replacement rolls back the profile container, not one isolated character slot. If progress disappears or rolls back, If a restore is replaced on launch, compare Steam Cloud state and modification times. Keep the original local file before testing any imported container. Resolve identity/path/cloud questions first. A cloud conflict is not proof that the save itself is corrupt, and a successful upload is not proof that files from another storefront are compatible.
Verification context: Windows path, S0000.sl2 filename, Steam Play behavior, and Steam Cloud support were reviewed against current PCGamingWiki coverage.