If you don't wait for complete synchronization, you won't lose bitcoins.  You'll just end up with a double spend that will never confirm.  Then you'll have to use a tool like pywallet to fix the wallet.

The real issue arises after you've sent about 100 transactions without replacing one copy of the wallet.dat with the other.    This problem is due to the way Bitcoin-Qt handles address generation and transaction change.  It won't matter if the blockchain is fully synchronized or not. At that time you'll have exhausted the pre-generated address pool, and you'll start to see extra bitcoins disappear out of the wallets.  The problem can be resolved safely if you are careful and know what you are doing.