You wont lose your balances. You will need to export your wallet into a special back up. Then after the upgrade you will import that file into the new wallet, and claim your balances. specifically if you are using version 0.9.3 you will need to go to the console
click your account name in the upper right hand corner.
click advanced
click the >_console button
type in
wallet_export_keys default.json
This will generate a file called default.json in the same folder you are running your BitShares client in.
Once you launch the new wallet you will import this file and claim your balances.