For Sync to use the same settings, it shall be looking and the same storage every time it starts - either to the .sync in current directly, or in "stoarage_path" in config.  Unfortunately, we don't know how you were launching BitTorrent and Resilio Sync, but the key point here is to use the same storage.  If you were installing package in both cases, then storage is used automatically.  if you were using a binary and moved to package, or vice versa, then new storage will be created. Or