I have the same problem. When I look at the error log, the following is reported, but means nothing to me.
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!ENTRY org.eclipse.ltk.core.refactoring 4 10000 2016-06-23 15:07:24.367
!MESSAGE Internal Error
!STACK 0
java.lang.NullPointerException
at org.eclipse.cdt.internal.corext.codemanipulation.InclusionContext.<init>(InclusionContext.java:64)
at org.eclipse.cdt.internal.ui.refactoring.includes.IncludeCreationContext.<init>(IncludeCreationContext.java:42)
at org.eclipse.cdt.internal.ui.refactoring.rename.HeaderFileReferenceAdjuster.createEdit(HeaderFileReferenceAdjuster.java:237)
at org.eclipse.cdt.internal.ui.refactoring.rename.HeaderFileReferenceAdjuster.createEdit(HeaderFileReferenceAdjuster.java:229)
at org.eclipse.cdt.internal.ui.refactoring.rename.HeaderFileReferenceAdjuster.addFileChange(HeaderFileReferenceAdjuster.java:204)
at org.eclipse.cdt.internal.ui.refactoring.rename.HeaderFileReferenceAdjuster.createChange(HeaderFileReferenceAdjuster.java:183)
at org.eclipse.cdt.internal.ui.refactoring.rename.HeaderFileRenameParticipant.checkConditions(HeaderFileRenameParticipant.java:110)
at org.eclipse.ltk.core.refactoring.participants.ProcessorBasedRefactoring.checkFinalConditions(ProcessorBasedRefactoring.java:257)
at org.eclipse.ltk.core.refactoring.CheckConditionsOperation.run(CheckConditionsOperation.java:85)
at org.eclipse.ltk.core.refactoring.CreateChangeOperation.run(CreateChangeOperation.java:121)
at org.eclipse.ltk.core.refactoring.PerformChangeOperation.run(PerformChangeOperation.java:209)
at org.eclipse.core.internal.resources.Workspace.run(Workspace.java:2313)
at org.eclipse.ltk.internal.ui.refactoring.WorkbenchRunnableAdapter.run(WorkbenchRunnableAdapter.java:87)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:122)
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This is with KDS version 3.1.0