I'm having this issue since ever with FB 4.7 (the normal IDE version, not the command-line one).
The most consistent way I found to resolve it is to delete the output folders of all flex projects, then restart and perform a clean build.
My suspect is that the incremental compilation is flawed, but cannot be sure of it.
P.S. usually the initial error has this root exception
Root exception:
java.lang.NullPointerException
at com.adobe.flexbuilder.codemodel.internal.bridge.WorkspaceSpecification.getStateLocation(W orkspaceSpecification.java:157)
at com.adobe.flexbuilder.codemodel.internal.bridge.WorkspaceSpecification.getFileInStateLoca tion(WorkspaceSpecification.java:149)
at com.adobe.flexbuilder.codemodel.internal.search.AbstractTextDatabase.start(AbstractTextDa tabase.java:81)
at com.adobe.flexbuilder.codemodel.internal.search.ASSearchDataProvider.<init>(ASSearchDataP rovider.java:25)
at com.adobe.flexbuilder.codemodel.internal.search.SearchIndexManager.initialize(SearchIndex Manager.java:155)
at com.adobe.flexbuilder.codemodel.CMCoreActivator.activate(CMCoreActivator.java:189)
at com.adobe.flexbuilder.codemodel.CMCoreActivator.start(CMCoreActivator.java:76)