What you want to do is aggregate assembly. Try setting the same assembly identifier for each module, and then pass the value -Dfortify.sca.toplevel.artifactId as the artifactID of the parent POM. This should give you one FPR file. It should look like this:
mvn clean
mvn -Dfortify.sca.buildId=ACMEPortal com.fortify.ps.maven.plugin:sca-maven-plugin:<version>:clean
mvn -Dfortify.sca.buildId=ACMEPortal package com.fortify.ps.maven.plugin:sca-maven-plugin:<version>:translate
mvn -Dfortify.sca.Xmx=800M -Dfortify.sca.buildId=ACMEPortal -Dfortify.sca.toplevel.artifactId=AcmePortal com.fortify.ps.maven.plugin:sca-maven-plugin:<version>:scan
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