once the wallet is in sync then is the only time you will see any pending incoming transactions arrive…and as long as your wallet contains the address you had the coins sent to then your coins will be there
if your coins are not in the wallet then the wallet does not contain that address that the transaction belongs to…you need to import the address you sent the coin to into your synced wallet using the private key…or if you are using a backup then make sure that your backup is in the appdata folder for Litecoin and renamed wallet.dat and that there is only one wallet.dat file in the appdata folder…folder located at : c:/(current user)/AppData/Roaming/Litecoin by defalut