As long as you save it somewhere after you get the BT the BTs are saved to your gamertag. So even if you're on your 5th playthrough on Chaos, if you go back to an original save on Earth for example your first playthrough, they will still be there. The same goes for spaceship data, weapons and monsters.
So if you get Gabriel's jewel on one playthrough you can even turn that into a monster jewel on your chaos or universe playthrough. Which is totally what I did.
The only boss I've had real issues with is that boss in the insect warren; fuck him in the Wandering Dungeon too. Thing pisses me off. Other then that, I haven't had much trouble with other bosses (I beat Gabriel at level 113, everything else was a breeze, though Gabriel took me two tries because the first time I just wanted to see what he did that was different) and the Eth queen I had down very very far but ended up messing up and will do later on I'm sure without an issue. Working on getting a super tri-emblum for her atm.
Does anyone know what the second to last monster is in the monster collections? I know (I forget if its 154 or 254, but I'm talking about the very end) the last one is likely the Eth. queen but I haven't bumped into the one before that so was wondering if anyone knew.
edit: nevermind, FML, doing team battle arenas.
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