On Windows, saves are stored in a location outside of the game directory. Just download and run the new version and it will pick up existing saves.
On Android, install the new APK over the old one. Newer builds will happily replace older ones while keeping your saves intact. Don't uninstall the old version or you'll lose the saves.
I assume Mac and Linux work the same way as Windows but that's an engine thing, not something specific to Sileo, so I couldn't tell you specifics.