I assume you have deployed this application on Netweaver correct? In this case there is a property that is supposed to get set when you deploy the application. If for some reson this was done incorrectly and then fixed it is possible the property is not in synch. The property is: system.application.path. This property can be maintained directly in Netweaver using Configtool. Check the value of this property. If it is not correct, fix it and restart the application. The emails should then have the correct URL.
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