Although you did not indicate the nature of the application. I mean what you do. What I get from the question is that you are using an HTA application, which means that the application requires access to the system level. Now, since Linux and Windows are completely different platforms. It is not possible to run one application from one platform to another.
If you can work at the plugin level, such as developing a flash plugin, or you can use Adobe AIR to create your application.
I want to say that do not use Microsoft native code in your application.
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