Is it a linux computer or a NAS, or Windows Service? Most likely it's a linux, right?  the thing is that when you start Sync, it uses a new storage folder (the .sync folder where all settings are stored). Sync creates a storage in current directory (your pwd), or uses one from a config (if it's launched with a config).  So for you, check out for multiple storages across your desktop, and point the binary to the old storage either with --storage /path argument, or using config