No, your previously used addresses will not be affected. What the message is referring to is the pool of unused addresses, which is what allows old backups to still work even if you've created new addresses in the meantime. This pool of unused addresses is wiped and recreated when you encrypt your wallet or change your passphrase, meaning if you create a new address in your encrypted wallet, this new address will not be present in your old backups (it otherwise would be).

Note that the pool only contains 100 addresses by default, and for technical reasons a new (hidden) address is created each time you send coins, so you must backup your wallet regularly whether you've encrypted it or not.

Click Inputs under Coin Control when sending coins, and select which address(es) to use.