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This problem occurs when refactoring a class name and renaming the file. Sometimes the file name will change but the refactoring of the class name else where fails. I have found that if I uncheck the rename file option, refactoring works every time but I am forced to rename the file myself. What appears to be happening is a race condition where the file is renamed before the refactoring of the class. When this happens the class name is not changed anywhere else. This problem happens to me about 80% of the time.
Seems to me to be a duplicate of issue #255649. Thanks. *** This bug has been marked as a duplicate of bug 255649 ***