I ran into the same problem yesterday. All of a sudden it didn't work anymore.
The trick for us was to run a complete baseline_update. After that, the partial-update worked as expected again (???)
But it did not work for me. I tried running baseline update many times. Even after that partial update ended with the same error message.
Then I changed the name of the file in all the places. It worked then. But still unable to find out what is the reason for this error and where does endeca hold the old file names even though it does not exist any more.