I would also say that "September 6th 2011 through October 6th 2011" suggests that October 6th was meant to be the last day of his annual leave. However, the original says that he was actually due to resume work on October 6th, making October 5th the last day of his annual leave.
I would say:
"Please be advised that Mr John Doe commenced annual leave on September 6 2011. He was scheduled to return to work on October 6 2011. He failed to do so, nor has he made any contact with the office/company [this will depend on the setup of your company].
Please commence proceedings to terminate his employment with immediate effect."