Look up your neo-GUI wallet address in the blockchain at https://neotracker.io. You should see your neo there. The old neo-GUI wallet takes some time to sync so be patient.
You should migrate your neo to the new NEON wallet too when you get a chance and after you locate your coin. https://github.com/CityOfZion/neon-wallet
RE: NEO (Antshares) Windows neo-gui Wallet is Missing Transactions and Coin