Well... poké balls have* to be able to contain items in some way, shape or form, don't they? How else do you explain your sneasel holding on to those blackglasses even after it's been recalled? Dunno how the mechanics of that would work because "wat make pokeyball go" is not an area of headcanon I've spent a lot of time on, but it is right there in the games if you'd like to try and expand on that or something. *shrug*
*I guess you could specify that the item is automatically rejected by the ball and dropped while the pokémon itself is pulled inside, but then that means the trainer would have to put the item back on every time they sent the pokémon out again. Doesn't appear to happen that way, does it?
I'm not sure what you're writing, but I guess I'd first ask you to think about why it was necessary to have the note in a poké ball in the first place. (Possibly not that necessary since you seem to have found a way around it; either way, you don't have to elaborate here if it's spoilery, just think about it.) Then, if you're still attached to the idea of note-in-ball but don't want to deal with the implications of "catching" items, I'd ask whether it's possible that a pokémon hold the note—almost like the mail feature in the games. Again, I don't know how well that works in the context of whatever your situation is, but I can see certain types of characters either handing off a note in a ball "oh and also there's a free eevee but mostly just read the note", or even making a quick capture for the explicit purpose of holding the note. The latter especially is a hilariously convoluted way to go about delivering a message, but now I have character bunnies about the sort of person who would beat up and catch an innocent, minding-its-own-business rattata just to give a note to someone else so it can't be all bad.
Actually, now that I think about it, even if the ball couldn't actually digitize or convert or blah blah blah science whatever an item, couldn't you just put the note inside it anyway? In essence it's nothing more than a hollowed-out sphere, a vessel just like any other; far as I can tell you can open it without explicitly triggering its capture mechanism, or if the mechanism is tripped then it can still remain open without having successfully pulled anything inside. So... put the note inside it as you'd put it inside any other container, and just don't have the mechanism go off because there're no pokémon involved. (Or maybe, if you do want items to be affected in general, you could use a ball with a broken capture mechanism.) Unless it's necessary that the note actually be "caught" by the ball as opposed to just stored within it, that seems like an easy way to solve your problem.