/shrug, It's happened to me twice once was a .txt file in the info center and the other was two of the font files. I thought it odd myself but /shrug I have seen computers do odder things. Being java is managed code there is no telling what happened.
Here is the exact error message you get when you try to update after it does it.
Exception thrown while checking file hash
Code:
java.io.FileNotFoundException: C:\Program Files\Sony\EverQuest II\UI\ProfitUI\fonts\Highspeed.ttf (Access is denied)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(Unknown Source)
at com.twmacinta.util.MD5.getHash(MD5.java:763)
at de.pala.updater.IO.Filesystem.checkFile(Filesystem.java:122)
at de.pala.updater.Arrange.IO.checkFile(IO.java:168)
at de.pala.updater.Files.checkFiles(Files.java:75)
at de.pala.updater.GUI.Main$UpdateThread.run(Main.java:738)