This is expected behaviour of distributing documents using publisher. You will not be able to see the Script after distribution.
That's the reason you should keep folder structure like Source and Destination. Reload your document in Source folder and publish it to Destination folder and Access point should be configured to point Destination folder.
This way you will always have you native code (apps) in Source folder and publish docs (without script) destination folder.
Use following path to set up Source Folder-->Management Console--> System--> Setup--> Distribution Services--> General--> Source Folder
To Setup Destination folder-->Management Console--> System--> Setup--> QlikView Services--> Folders--> Mounted Folders--> Name (Destination or Published Documents) and give the path C:\Folder_Name
As annafuksa1 mentioned, that is how distribute works. Do you have folder structure defined? General practice to distribute is, the QVW file in 'DataModel' folder will be reloaded and distributed to another folder say 'Application'. QVW in 'DataModel' folder contains both Script and Presentation layer. where as QVW in 'Application' folder contains only presentation layer which will be made available for users on Access point. Every reload task, updates the file in 'DataModel' folder and distributes it to 'Application' folder.