The error you are seeing means you do not have access to the code 
<https://cloud.google.com/appengine/docs/python/tools/uploadinganapp?hl=en#Python_Downloading_source_code>
. 

For sanity sake I tested this:

Created a fresh app
Create 2 modules (modulea, moduleb)
Uploaded using appcfg.py update app.yaml modulea moduleb
Confirmed all pages worked
Downloaded using: appcfg.py download_app -A app-id-here .
All files for ALL modules are present.

What I think is happening with you is you are confusing App Engine modules 
<https://cloud.google.com/appengine/docs/python/modules/> and company 
decided modules. Do they have different app ids?

On Tuesday, August 4, 2015 at 6:32:00 AM UTC-4, Paul Canning wrote:
>
> I know you can download your default module code using "appcfg.py 
> download_app" and even a specific version of the default module.
>
> Nut is it possible to download the code of a MODULE?
>
> E.G I have the the default app, Website A. I thne have a module, which is 
> an entirely different site, Website B.
>
> The appcfg.py command will only let me download versions of Website A.
>
> Here is the usage:
>
> "Usage: appcfg.py [options] download_app -A app_id [ -V version ] 
> <out-dir>"
>
> See, no options for module.
>
> So, how can I download specific module code?
>

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