Any time you choose different settings in W3TC it is possible W3TC will create new or additional W3TC htaccess code. You would copy the new or additional W3TC htaccess code to BPS Custom Code and do all the Custom Code steps again.
@ Alex – W3TC setup with BPS is completely automated now.
UPDATE: BPS Pro 13+ and BPS 2.0+ versions have a feature called: Setup Wizard AutoFix (AutoWhitelist|AutoSetup|AutoCleanup) that automatically creates plugin and theme whitelist rules and automatically sets up and cleans up caching plugins htaccess code.