From what I have read Bone Charms randomize (25 out of 35) at the start of a new game. Does this set the pool for the entire game? I know you can restart a mission and it will reset the bone charms, but is it only reseting out of the same pool of 25 (or the full 35)?

From my experience, it only randomize the bone charms the first time you enter a level.

So if you load the beginning of a mission and play twice, and reach a second level area of the mission, there will be different bone charms.

My only question is when it randomizes, does it pull from a pool of 25, or does that full 25 reset when you reset the level.

Hm, that's a very hard one to test, actually. I didn't even know there was a selection from a full 35 Charms pool.
It's almost impossible to test, except maybe by saving manually before grabbing *each* charms in the game, and writing down what you got. After that you would have to do some reloading/restart mission/restart game mumbo-jumbo, going through each of your manual saves and writing down the result for each and every 25 charms. Then by comparing your results you would get an idea...

But it's an extremely tedious operation, really, and I'm not even sure how "start new game" works, compared to "reloading a mission". If you start a new game, but then immediately jump back to your saves, instead of loading straight from the menu, does that affects anything? I really am clueless.

(Nearly) Impossible to test? About what I figured. Guess I can just fish for the ones I want in the first two missions and hope I get lucky...eventually.