If they already have full masteries, they can't receive scrolls - so none will be wasted.
However - I'd strongly recommend that you use as few fully-leveled champs as possible. That way, you get to double-dip - while farming for scrolls, you'll also be getting XP to level them. In a perfect world, you'd have five champs that are all leveling while getting masteries - but that's not going to be feasable in many cases. But far more likely should be to use only one level 60, with the others being leveled - or, worst-case, using two level 60s.
If they already have full masteries, they can't receive scrolls - so none will be wasted.
However - I'd strongly recommend that you use as few fully-leveled champs as possible. That way, you get to double-dip - while farming for scrolls, you'll also be getting XP to level them. In a perfect world, you'd have five champs that are all leveling while getting masteries - but that's not going to be feasable in many cases. But far more likely should be to use only one level 60, with the others being leveled - or, worst-case, using two level 60s.
That was helpful, thanks!