Keystore file exists but is empty?

I had exectly the same problem. Issue appear when you give path to keystore file without the file name. You have to give keystore file name with the path after -keystore option. This means in your case:

keytool -exportcert -alias freenthrowkey -keystore C:\Users\User\Documents\FreeNthrowkey\KEYSTOREFILENAME.jks

Using following commands should give you proper output:

keytool -list -keystore .keystore

If you are looking for a specific alias, you can also specify it in the command:

keytool -list -keystore .keystore -alias foo

Also, to generate signed APK I suggest you to use Android studio itself. Choose "Generate Signed APK" from Build menu of Android studio and follow the steps. It will generate proper keystore at given path.