You can't delete the embedded library.
However you can delete the contents of the embedded library.
Did it crash as soon as you hit the delete button or only when you re-loaded the library?
If the later then maybe it was something vital to the model (I have no idea what it could be).
The file won't have saved, so re-open it and delete just a few items at a time to see if you can work out what it is.
Or open the BPN (backup) file and try that.
Did the bug report appear?
If so send it off and then follow up with your local support centre with the bug number and ask them what the problem was.