It happened to me a couple of times - I also like long saves and after some decades you can have a lot of money. However, with me it was usually the sale of 1-2 players for really big bucks that tipped the transfer funds into negative, and the next time the board allocated the transfer budget, it was OK again. There could be a similar workaround as with funds, where the board just "invests" the money once you get over a billion. There could be a coded hard limit of 1 billion and your transfer budget doesn't increase even if you sell someone.