Engineer to Logical Model in SQL Developer EA4 causes problems

I'm working with SQL Developer 3.0 EA4 (Build MAIN-03.97)
Unfortunately I fond out, that it would be impossible to use the function " Engineer to Logical Model" any more after I change the relational model. In datamodeler.log I got the error message line "[AWT-EventQueue-0] ERROR MDBAction - java.lang.NullPointerException" for each time I use the function "Engineer to Logical Model". I try it out with the sample model "sh_cre_all.sql" and with following steps:
1) Import via DDL File – no problem
2) Engineer to Logical Model – no problem
3) Change some attributes in the relational model – no problem
4) Again Engineer to Logical Model – no problem
5) Save, Exit an Open the sample – no problem
6) Again Step 3 and 4 – no problem
7) Add a table via drag&drop from an oracle schema – no problem
8) Save, Exit an Open the sample – no problem
9) Engineer to Logical Model no longer possible!!!
Bernd

I have experienced similar problems with 'Engineer to Logical model'.
The scenario was following:
Creating Logical model using 'Engineer to Logical model' from existing Relational model.
Modifying the Relational model and 'Engineer to Logical model' again. No exception occured but the Logical model wasn't updated accordingly.
Removing all entities from the Logical model.
Trying to 'Engineer to Logical model' again. No entities were created in the Logical model (even after few tries).
So I got to situation where I was unable to generate a Logical model, which was quite frustrating.
The workaround was to create new Data Modeller project and import to it from the original project - the 'Engineer to Logical model' worked again.

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    vSelectionListener.java:829)
            at oracle.dbtools.raptor.oviewer.base.NavSelectionListener.openEditor(Na
    vSelectionListener.java:749)
            at oracle.dbtools.raptor.oviewer.base.NavSelectionListener.access$1500(N
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            at oracle.dbtools.raptor.oviewer.base.NavSelectionListener$4.run(NavSele
    ctionListener.java:476)
            at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:727)
            at java.awt.EventQueue.access$200(EventQueue.java:103)
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            at java.awt.EventQueue$3.run(EventQueue.java:686)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDo
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            at oracle.javatools.internal.ui.EventQueueWrapper._dispatchEvent(EventQu
    eueWrapper.java:169)
            at oracle.javatools.internal.ui.EventQueueWrapper.dispatchEvent(EventQue
    ueWrapper.java:151)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre
    ad.java:242)
            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
    java:161)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
    ad.java:150)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
            at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
    "AWT-Windows" daemon prio=6 tid=0x0000000009a09800 nid=0x1084 runnable [0x000000
    000a52f000]
       java.lang.Thread.State: RUNNABLE
            at sun.awt.windows.WToolkit.eventLoop(Native Method)
            at sun.awt.windows.WToolkit.run(WToolkit.java:299)
            at java.lang.Thread.run(Thread.java:722)
    "AWT-Shutdown" prio=6 tid=0x0000000009a04800 nid=0x11dc in Object.wait() [0x0000
    00000a42f000]
       java.lang.Thread.State: WAITING (on object monitor)
            at java.lang.Object.wait(Native Method)
            - waiting on <0x00000000f39cc0b8> (a java.lang.Object)
            at java.lang.Object.wait(Object.java:503)
            at sun.awt.AWTAutoShutdown.run(AWTAutoShutdown.java:287)
            - locked <0x00000000f39cc0b8> (a java.lang.Object)
            at java.lang.Thread.run(Thread.java:722)
    "Java2D Disposer" daemon prio=10 tid=0x0000000009a02000 nid=0xedc in Object.wait
    () [0x000000000a32f000]
       java.lang.Thread.State: WAITING (on object monitor)
            at java.lang.Object.wait(Native Method)
            - waiting on <0x00000000f3c0dc20> (a java.lang.ref.ReferenceQueue$Lock)
            at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
            - locked <0x00000000f3c0dc20> (a java.lang.ref.ReferenceQueue$Lock)
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            at sun.java2d.Disposer.run(Disposer.java:145)
            at java.lang.Thread.run(Thread.java:722)
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    0000000000000]
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            - waiting on <0x00000000f3a05b40> (a java.lang.ref.ReferenceQueue$Lock)
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    "GC task thread#1 (ParallelGC)" prio=6 tid=0x000000000236f800 nid=0x6a4 runnable
    "GC task thread#2 (ParallelGC)" prio=6 tid=0x0000000002371000 nid=0x131c runnabl
    e
    "GC task thread#3 (ParallelGC)" prio=6 tid=0x0000000002373000 nid=0x1508 runnabl
    e
    "GC task thread#4 (ParallelGC)" prio=6 tid=0x0000000002376800 nid=0x1608 runnabl
    e
    "GC task thread#5 (ParallelGC)" prio=6 tid=0x0000000002377800 nid=0xdf4 runnable
    "GC task thread#6 (ParallelGC)" prio=6 tid=0x0000000002379000 nid=0x1518 runnabl
    e
    "GC task thread#7 (ParallelGC)" prio=6 tid=0x000000000237a000 nid=0xf50 runnable
    "VM Periodic Task Thread" prio=10 tid=0x0000000009803800 nid=0xfa4 waiting on co
    ndition
    JNI global references: 1712
    Heap
    PSYoungGen      total 65984K, used 49680K [0x00000000fbd60000, 0x00000000fffd00
    00, 0x0000000100000000)
      eden space 63872K, 77% used [0x00000000fbd60000,0x00000000fed7b368,0x00000000f
    fbc0000)
      from space 2112K, 19% used [0x00000000ffbc0000,0x00000000ffc28fd8,0x00000000ff
    dd0000)
      to   space 1984K, 0% used [0x00000000ffde0000,0x00000000ffde0000,0x00000000fff
    d0000)
    ParOldGen       total 124928K, used 103514K [0x00000000f3800000, 0x00000000fb20
    0000, 0x00000000fbd60000)
      object space 124928K, 82% used [0x00000000f3800000,0x00000000f9d16be0,0x000000
    00fb200000)
    PSPermGen       total 116160K, used 85069K [0x00000000e3800000, 0x00000000ea970
    000, 0x00000000f3800000)
      object space 116160K, 73% used [0x00000000e3800000,0x00000000e8b137b0,0x000000
    00ea970000)
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            at oracle.ideimpl.log.TabbedLogManager$4.run(TabbedLogManager.java:321)
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       java.lang.Thread.State: TIMED_WAITING (on object monitor)
            at java.lang.Object.wait(Native Method)
            - waiting on <0x00000000f4f28660> (a java.util.TaskQueue)
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    "TimedCache-Timer" daemon prio=6 tid=0x000000000b530000 nid=0x156c in Object.wai
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            at java.lang.Object.wait(Object.java:503)
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       java.lang.Thread.State: WAITING (on object monitor)
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            - waiting on <0x00000000f3e58220> (a org.eclipse.osgi.framework.eventmgr
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            at org.eclipse.osgi.framework.eventmgr.EventManager$EventThread.getNextE
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            at java.lang.Thread.run(Thread.java:722)
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            - locked <0x00000000f3bfd160> (a java.lang.ref.ReferenceQueue$Lock)
            at org.openide.util.lookup.implspi.ActiveQueue$Daemon.run(ActiveQueue.ja
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    "TimerQueue" daemon prio=6 tid=0x0000000009ade800 nid=0xc6c runnable [0x00000000
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            at org.openide.filesystems.FCLSupport$DispatchEventWrapper.dispatchEvent
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            at org.openide.filesystems.FileObject$ED.dispatch(FileObject.java:1314)
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            at org.netbeans.core.windows.WindowSystemImpl.save(WindowSystemImpl.java
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            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.
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            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
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            at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:135)
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    "Attach Listener" daemon prio=10 tid=0x00000000097df800 nid=0x15f8 runnable [0x0
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    "Signal Dispatcher" daemon prio=10 tid=0x00000000097de800 nid=0x161c waiting on
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            - waiting on <0x00000000f39fbe28> (a java.lang.ref.ReferenceQueue$Lock)
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            - locked <0x00000000f39fbe28> (a java.lang.ref.ReferenceQueue$Lock)
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    "GC task thread#4 (ParallelGC)" prio=6 tid=0x0000000002376800 nid=0x1608 runnabl
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