It looks at size, modification time and optionally permissions to detect changes. You can query GET /rest/db/file — Syncthing documentation on the device showing the locally changed items (for instructions: [ How To ] call the REST API from Windows PowerShell).
Possibly that is a filesystem following a pattern Syncthing dislikes: It might store high-precision timestamps in memory when Syncthing sets the modification time, and once that’s erased (restart) it lost that information and shows lower-precision timestamps. Which Syncthing detects as a chang.