I'm just finished up the bonus series but during it I picked up The Hunt for Lord Tharsis. I was on the part where I had to kill Apprentice Loell. I did a few more quests then I logged off. When I logged back in the next day I still had the Balmorra Bonus series but the Apprentice Loell and Hunt for Tharsis sub quests were gone from my mission log. I opened a help ticket but they only told me to go back to the quest giver and get the quest again. I have been all over Balmorra to every quest giver I can think of but no luck

 

Is it timed and if you don't do it within the allotted time it just disappears never to gotten again?

As usual, the CS rep had no idea what they were talking about. Hunt for Lord Tharsis is the bonus sub-quest for Balmorra: Bonus Series 1. Note the numeral, as there are two bonus series questlines on Republic Balmorra. Having a bonus sub-quest for a bonus series is confusing, and this is the first planet I've seen that did it. After you finish the quests associated with Series 1, it will send you back to talk with the Twilek woman, Wixx I think. She will finish the Series 1 questline and immediately give you Balmorra: Bonus Series 2. As with all bonus sub-quests, when you finish the parent quest you lose the sub-quest if you haven't completed it yet. Most likely that is what happened and you didn't realize it. So double check your tracker and see if it says Series 2.

Yeah this happened to me too. After Lord Tharsis owned my sorry arse and nobody was around to help me kill him I decided to finish the bonus mission of the bonus series 1 later and wanted to continue with the quest. Unfortunately talking to the quest giver ended bonus series 1 and so I couldn't finish the bonus of the bonus anymore. That's when I decided to always finish the bonuses before talking to quest givers again.