An error will occur if you try and host a web application within a web site and mix the .Net versions. This is because the virtual application will attempt to inherit from it's parent. This can be switched off by editing the parent web.config as follows:
Wrap <system.web> with:
<location path="." inheritinchildapplications="false">
For Example:
<location path="." inheritinchildapplications="false">
<system.web>
...
</system.web>
</location>
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