I've been trying to buy train tickets on-line from Zagreb, Croatia to Sarajevo, B-H in September without success. Is this option not available?
Yes, you might look into the bus. Or flying, believe it or not, which may not be that expensive.
If you bus, consider stopping on the way in a little town like Jajce, if perhaps you can arrange a good bus connection that way.
Is this option not available?
Quoting the most reliable source for train travel in the Balcans, the Man-in-seat-61:
IMPORTANT UPDATE 2017: It's now confirmed that the Zagreb to Sarajevo train has been discontinued completely as from 11 December 2016, leaving Bosnia completely cut off from the rest of the European network. It's not clear why, and there has been no advance notice. It seems agreement between Bosnian and Croatian railways wasn't reached in time. Further updates will be posted here when known...
Another nice train route gone ...