Why Does My Virtual Directories Disappear When I Reboot My Webrolesite Instance From Azure Management Portal?

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Azure

deployment

Hi,
I have a scenario here. Please assist me for a permanent solution.
I have an application hosted on azure. say abc.com. I have created a virtual directory over there via Remote Connection through azure management portal say: abc.com/aa.

1) When i reboot the webrolesite and webroleemail instances from the azure management portal, my virtual directory disappears and i need to re-create and map it back.
It too risky as both the applications are in production stage.

2) When i build a package from the visual studio for my azurecloud application, the are two files that get generated in the release folder: package file, configuration file.
Same as the point 1, when i upload the package via update the instance files in azure management portal, the virtual directory disappears.

Thanks.