With the ability to level up quickly even for high level players, more and more players will be hitting high levels of 700+. With that high level, notes gained from missions and bonuses continue to increase. The 2,147,483,647 hard limit is easily reached forcing a player to spend notes or lose them. Even spending all those notes on skills, we can barely get 600 skills.
Since this is a 32-bit hard limit, I am guessing rewriting all of the code to 64-bit is not an easy task.
Another option I thought of is having a secondary spot to save notes, kind of like a bank. We could then store another 2.1 billion notes in that spot. It would be similar to buying a tab to store extra items in. Thus we could transfer notes from regular-to-bank or withdraw from bank-to-regular area as long as neither area maxes out.