I found the following JIRA, where it is described, that it is possible to use different filter files for normal execution and for testing.
The problem is I don't get how this has to be configured.
<build>
<filters><filter>myfilters.properties</filter></filters>
...
<resources>...</resources>
<testResources>...</testResources>
<build>
This way the filter is applied to all resources, but I like to have is separate filters definitions for resources and testResources.
I am using maven 3.0.5.