Fix: File target doesn't duplicate header in archived files #245

To fix issue #245 I first looked at the suggestion made by johnnyjob to remove the filename from initializedFiles en decreasing the initializedFilesCounter by one. This seemed too blunt for me. 
It turns out that the only time a header line should be written again is after a file has been moved (archived). The total amount of initialized files in initializedFilesCounter should never be altered for this fix, otherwise the amount would never trigger a CleanupInitializedFiles()