I've been able to re-pro this with a bare bones core data document
app for the both the XML store and the binary store, the SQLLite
store seems to be ok.
You can download the re-pro case from http://www.pocketsoap.com/osx/emptyFile.zip
run it, enter some text, select save, and choose either XML or
binary format. look at the file, it'll be fine. now select save
again, now the file will be 0k long. (radar #/5575683)
That appears to be a genuine, rather unpleasant, bug. Thanks for the
report.
A trivial workaround for now would probably be simply to implement: