Without knowing what caused your (new-) save-game loss the only thing you can do is backing up.
You have several options:
- Backup manually, copying your save-game files to a save place
- Backup via script, write a file-copying script
- Run it manually
- Run it via Cron/Tasks
- Use a file backup/copy software
- For manual run
- Which runs in the background and does automatically
- Version your files in-place with a VCS, like Git, HG, Bzr etc. You won’t have duplicate files and confusion this way, just a repository-folder with the files history.
Alls this of course only works if your game actually saves after you played. If it does not even save that is your problem, and you can’t do anything about losing game-state until you solve that.
The savegame files should be in
C:\Program Files\Ubisoft\Ubisoft Game Launcher\storage for x86 systems, and in
C:\Program Files(x86)\Ubisoft\Ubisoft Game Launcher\storage for x64 systems.
According to a video, that folder also includes a temp folder, which includes a save for each checkpoint. That way, you can rename your recent temp checkpoint file to a savegame, put it in your savegame folder, and then load it.