>
> Nope. You wouldn’t be overriding the wsgi.conf file, but adding a new conf 
> file in same directory. Apache will load files when using Include with 
> wildcard in alphabetical order. You can therefore name the file such that 
> is ordered before wsgi.conf. It will load that first. You can then rely on 
> fact that Apache will use the first VirtualHost it finds when name based 
> virtual hosts aren’t actually being used, which is the case here as the 
> generated VirtualHost lacks a ServerName directive. You can therefore 
> provide your own separate VirtualHost set up how you need it.
>

This is a good advice, it would certainly allow me to add the timeout 
setting and any other setting I could need for the WSGIDaemonProcess 
directive. The only issue is that I need to match the exact settings and 
file paths the amazon file uses, and if they change it for some reason 
everything would stop working from one day to another, but I guess they 
shouldn't change it at all unless the machine version is updated.
I will keep this idea as a last resource if I'm not able to find out the 
exact cause of the process not being killed. I still have a few things to 
test before giving up on finding the exact cause.


Which of those two directories is wsgi.conf in?
> What else is in those two directories?
>

wsgi.conf is at conf.d, at least the one with the virtual host and all 
wsgi.conf setup
There's also another wsgi.conf at conf.modules.d but all it does is load 
the wsgi module.

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