I am a TH9 CoC player, and I got confused also the first time when I saw the overflowing Season Bank Loot. But the thing is that the EXTRA loot still stays. Like your Storage of Gold is 4,000,000 and you have 3,000,000. Your season bank is 5,000,000. So you then have 8,000,000 gold even if your storage is only half the cash. But when it becomes 7,999,999 gold, it's not becoming 8,000,000 again.