Eclipse plugin referencing old sub projects on project import

I have a project with many sub-projects.
I import the project with only some sub-projects and everything works as expected.
I then delete a sub-project locally and checkout another sub-project.
An exception is generated referring to the old project.
To verify the project structure I execute gradle eclipse without problems.
Then I try import Existing Projects or import Gradle Project and on refresh an exception is generated:

ENTRY org.springsource.ide.eclipse.gradle.core 4 0 2015-07-24 16:37:14.086
!MESSAGE Project location doesn't exist: /home/corneil/eaf/environment/development/develop/libraries/configuration
!STACK 0
java.lang.IllegalArgumentException: Project location doesn't exist: /home/corneil/eaf/environment/development/develop/libraries/configuration
        at org.eclipse.core.runtime.Assert.isLegal(Assert.java:63)
        at org.springsource.ide.eclipse.gradle.core.GradleProject.<init>(GradleProject.java:131)
        at org.springsource.ide.eclipse.gradle.core.GradleProjectManager.getOrCreate(GradleProjectManager.java:67)
        at org.springsource.ide.eclipse.gradle.core.GradleCore.create(GradleCore.java:167)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.HierarchicalProjectBuildStrategy.getBuildFamily(HierarchicalProjectBuildStrategy.java:137)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.HierarchicalProjectBuildStrategy.predictBuildFamily(HierarchicalProjectBuildStrategy.java:148)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.GradleProjectModelManager.lockFamily(GradleProjectModelManager.java:156)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.GradleProjectModelManager.getModelInternal(GradleProjectModelManager.java:121)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.GradleProjectModelManager.getModel(GradleProjectModelManager.java:100)
        at org.springsource.ide.eclipse.gradle.core.modelmanager.GradleModelManager.getModel(GradleModelManager.java:77)
        at org.springsource.ide.eclipse.gradle.core.GradleProject.getModel(GradleProject.java:576)