It is likely (and to be expected) that a firmware (or OS) upgrade will wipe any user data or settings.
These settings are not easily translated / adjusted across such an update. However, most tools will give such a warning before you proceed.
In more detail ..
Firmware Update (ROM code)
A firmware update will normally cause ALL user data, settings, and (custom loaded) applications to be lost. This is because many applications and your online identity (connection to e-store) are usually firmware specific.
Exceptions: For only a minor update it may be possible to just replace the firmware, and not disrupt the higher layers. This is only advice for developers and the truly adventurous.
Your specific case: You are attempting to replace the Telstra (big Australian telco) firmware with (possibly) later firmware. This will likely not include any Telstra specific applications, and you would need to re-register the phone (upon completion). By then ALL data, settings, and applications would have been lost.
Firmware Update (Android OS)
An Android update will normally attempt to retain ALL user data, settings, and (custom loaded) applications. But this is only true for minor update, as major changes will make your existing applications incompatible. For each application, the vendor may provide an update with support for the new version to convert (or import) any old data.
Exceptions: If you are attempting a major Android update (eg. from 3.2 to 4.0+) this will very likely not retain (in any useful form) any of your settings.
Your specific case: If you were using KIES to update Android from 4.0 to 4.0.4 (or similar) this should be as painless as OTA (over-the-air) updates (prompted on your phone). However, it is not clear from your description what type of 'firmware' (Android or ROM) it is suggesting.
Note: I have not used KIES, as it has no Linux support.
Look at syncing or backup tools, to save any user data (phone numbers, messages, etc.) to your PC. Any applications will be more of a problem, but will still available (in the online e-store) to again download.