The Bitcoin-QT wallet has the larger balance.
You could try sending the entre balance to a newly generated address on bitcoin-qt and check if any coins remain at blockchain.info. If the blockchain.info wallet gets zero balance after you do that, all is OK and there are no mixed up funds.
BTW: only do what I said if you're comfortable enough using pywallet, in case you need to delete the transaction from bitcoin-qt's wallet to get your coins back, if anything goes wrong.