Oh, I see.
I quickly searched for it, hoping that maybe some metadata (EXTH) of the mobi format would include the text directionality, but there doesn't seem to be any. I also checked in the KT framework for some obvious signs of "text directionality" support, but there are none
So it seems like you're indeed out of luck. The only thing I can suggest is that you contact the calibre authors and let them know about the issue of the TOC disappearing on conversion. Maybe they can help.