My question is if the rebel player uses a boon card, does the card carry over to the next mission or is it discarded from the game? The campaign I'm currently on, we play that it is discarded because it is the most conservative.

It says on the card "return to the game box".

So it is discarded and a once per campagne use.

Thats what I figured. Thank you

Some missions refer to the number of Banes/Boons... I am assuming that once the Rebels user their Boon, it does not contribute to this tally anymore, since it has been returned to the Game box?

Correct. It refers to the number of boons or banes in the play area.