These are interesting ideas, but it does seem to needlessly complicate things. I think the simple answer is that quills will disappear as you collect them. They can't reappear every time you enter the level like in Banjo-Kazooie because you give them to Trowzer. In BK, Bottle's moves were free. Some complex and unnecessary system or algorithm would have to be put in place to fix this.
For the people who want quills to reappear, remember that there will be a "New Game+" after beating the game normally once where all moves are unlocked. This is as close as we will probably get to the old BK note system.