Can IDEA import multiple maven multi module builds in the same project?

I have a project I am working on with the following structure:

pom.xml (com.project:master-pom)

module1-master.xml (com.project:submodule1-pom) 

module2-master.xml (com.project:submodule2-pom)

those three .xml are in the same directory. 

If you were to build a war for submodule 1 you would call > mvn package -f module1-master.xml
and for submodule 2 you would call > mvn package -f module2-master.xml

both modules have as submodules the same set of poms.

I know InteliJ does actually import the project as a maven project but we are facing a lot of problems with workspace stability, usually these are .class not found exceptions witch are resolved by manualy deleting the /bin (/target) folder and rebuilding the module. 
Should the maven build be refactored to have a single master pom (as currently it technically has 3) or there is some other problem that is occurring here ?